make[2]: Entering directory '/usr/local/amber22/AmberTools/test' ./test_at_clean.sh cd antechamber && make -k clean make[3]: Entering directory '/usr/local/amber22/AmberTools/test/antechamber' Cleaning all antechamber test subdirectories: find . -name "*.dif" -print0 | xargs -0 /bin/rm -f /bin/rm -f \ ash/antechamber.out \ ash/sqm.in \ ash/sqm.out \ ash/sqm.pdb \ bondtype/antechamber.out \ c60/antechamber.out \ charmm/antechamber.out \ fluorescein/antechamber.out \ fluorescein/sqm.in \ fluorescein/sqm.out \ fpph/antechamber.out \ guanine_amber/antechamber.out \ guanine_amber/sqm.in \ guanine_amber/sqm.out \ guanine_amber/sqm.pdb \ residuegen/ala_conf1.esp \ residuegen/ala_conf2.esp \ residuegen/ANTECHAMBER_AC.AC \ residuegen/ANTECHAMBER_AC.AC0 \ residuegen/ANTECHAMBER_BOND_TYPE.AC \ residuegen/ANTECHAMBER_BOND_TYPE.AC0 \ residuegen/antechamber.out \ residuegen/ATOMTYPE.INF \ residuegen/esout \ residuegen/espgen.out \ residuegen/NEWPDB.PDB \ residuegen/PREP.INF \ residuegen/punch \ residuegen/QIN \ residuegen/qout \ residuegen/RESIDUE_GEN_MAINCHAIN.DAT \ residuegen/RESIDUE_GEN_RESP.INPUT1 \ residuegen/RESIDUE_GEN_RESP.INPUT2 \ residuegen/RESIDUE_GEN_RESP.OUTPUT1 \ residuegen/RESIDUE_GEN_RESP.OUTPUT2 \ residuegen/RESIDUE_GEN_RESPGEN.DAT \ residuegen/RESIDUE_GEN.AC \ residuegen/residuegen.out \ sustiva/antechamber.out \ sustiva/leap.log \ sustiva/prmtop \ sustiva/sqm.in \ sustiva/sqm.out \ tp/antechamber.out \ tp/sqm.out make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/antechamber' cd mmpbsa_py && make -k clean make[3]: Entering directory '/usr/local/amber22/AmberTools/test/mmpbsa_py' cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 02_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 03_Alanine_Scanning && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 04_Per_Residue_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 05_Pairwise_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 06_NAB_Nmode && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 07_Comprehensive && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 08_Stability && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 09_APBS_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 10_QM_MMGBSA && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 11_3D-RISM && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 12_Membrane_Channel && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/mmpbsa_py' cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.clean cd ../src/FEW/examples/test && ./Run.few.clean cd ../src/cpptraj/test && make -k clean make[3]: Entering directory '/usr/local/amber22/AmberTools/src/cpptraj/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make[5]: Entering directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make[5]: Leaving directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make[4]: Leaving directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make[3]: Leaving directory '/usr/local/amber22/AmberTools/src/cpptraj/test' cd leap && make -k clean make[3]: Entering directory '/usr/local/amber22/AmberTools/test/leap' Cleaning all test directories: (find . -name "*.dif" -o -name 'leap.log' -o -name 'leap.out' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) /bin/rm -f x.lib lib94.out ions94.log ff94_prm.out ff94_prm.log ff94.log make test.params OPT=clean make[4]: Entering directory '/usr/local/amber22/AmberTools/test/leap' make[4]: Leaving directory '/usr/local/amber22/AmberTools/test/leap' make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/leap' cd leap/glycam/06j && ./Run.glycam clean cd leap/glycam/06EPb && ./Run.glycam clean cd leap/glycam/06j_10 && ./Run.glycam clean cd leap/glycam/06j_12SB && ./Run.glycam clean cd ../src/cpptraj/test && make -k test make[3]: Entering directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make test.complete summary make[4]: Entering directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make[5]: Entering directory '/usr/local/amber22/AmberTools/src/cpptraj/test' ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_General CPPTRAJ: General tests diffing distance.dat.save with distance.dat PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing rmsda.dat.save with rmsda.dat PASSED ============================================================== diffing phi2.dat.save with phi2.dat PASSED ============================================================== diffing PhiPsi.dat.save with PhiPsi.dat PASSED ============================================================== diffing test.crd.save with test.crd PASSED ============================================================== diffing a1.dat.save with a1.dat PASSED ============================================================== diffing test.rst7.213.save with Restart/test.rst7.213 PASSED ============================================================== diffing test.nc.save with test.nc PASSED ============================================================== diffing r4.dat.save with r4.dat PASSED ============================================================== diffing a2.dat.gz.save with a2.dat.gz PASSED ============================================================== diffing a3.dat.bz2.save with a3.dat.bz2 PASSED ============================================================== diffing r2.dat.save with r2.dat PASSED ============================================================== diffing r3-nofit.dat.save with r3-nofit.dat PASSED ============================================================== diffing r5.dat.save with r5.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Parallel CPPTRAJ: Parallel tests. diffing d1-12.dat.save with d1-12.dat PASSED ============================================================== diffing a1-6-12.dat.save with a1-6-12.dat PASSED ============================================================== diffing phi2.dat.save with phi2.dat PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing avg.rst7.save with avg.rst7 PASSED ============================================================== CPPTRAJ: Parallel test with trajectory offset diffing offset.dat.save with offset.dat PASSED ============================================================== diffing test.nc.save with test.nc PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Strip CPPTRAJ: One frame strip command test diffing dummy.pdb.save with dummy.pdb.1 PASSED ============================================================== diffing dummy.rst7.save with dummy.rst7 PASSED ============================================================== diffing strip.tz2.truncoct.parm7.save with strip.tz2.truncoct.parm7 PASSED ============================================================== CPPTRAJ: Unstrip (Lig/Rec/Complex) command test diffing strip.tz2.truncoct.parm7.save with complex.tz2.truncoct.parm7 PASSED ============================================================== diffing receptor.tz2.truncoct.parm7.save with receptor.tz2.truncoct.parm7 PASSED ============================================================== diffing ligand.tz2.truncoct.parm7.save with ligand.tz2.truncoct.parm7 PASSED ============================================================== diffing Ligand.crd.save with Ligand.crd PASSED ============================================================== diffing Receptor.crd.save with Receptor.crd PASSED ============================================================== diffing Complex.crd.save with Complex.crd PASSED ============================================================== CPPTRAJ: Multi frame strip command test. diffing res1.tz2.crd.save with res1.tz2.crd PASSED ============================================================== CPPTRAJ: Strip topology with PDB info diffing strip.pdb.chignolin.parm7.save with strip.pdb.chignolin.parm7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Broken Traj: Running broken trajectory. diffing goodrmsd.dat with badrmsd.dat PASSED ============================================================== CPPTRAJ: Compressed broken trajectory test diffing goodrmsd.dat with ziprmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_TrajinOffset CPPTRAJ: Normal trajectory read with offsets. diffing rem.crd.save with rem.crd.combined PASSED ============================================================== CPPTRAJ: Gzipped trajectory read with offsets diffing rem.crd.save with gzip.rem.crd.combined PASSED ============================================================== CPPTRAJ: Bzip2ed trajectory read with offsets diffing rem.crd.save with bzip2.rem.crd.combined PASSED ============================================================== CPPTRAJ: Start argument offset diffing phi.dat.save with phi.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_RemdTraj CPPTRAJ: CRD Replica Trajectory Run with offset diffing d1.offset.dat.save with d1.offset.dat PASSED ============================================================== CPPTRAJ: CRD Replica Trajectory Run diffing d1.crd.dat.save with d1.crd.dat PASSED ============================================================== CPPTRAJ: NetCDF Replica Trajectory Run test diffing d1.nc.dat.save with d1.nc.dat PASSED ============================================================== CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: CRD Replica Trajectory Run with remdout diffing d1.ensemble.dat.save with d1.ensemble.dat PASSED ============================================================== diffing temp0.crd.300.00 with temp.crd.0 PASSED ============================================================== diffing temp0.crd.384.30 with temp.crd.1 PASSED ============================================================== diffing temp0.crd.492.20 with temp.crd.2 PASSED ============================================================== diffing temp0.crd.630.50 with temp.crd.3 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] diffing test.rst7.3.save with test.rst7.3 PASSED ============================================================== diffing test.rst7.5.save with test.rst7.5 PASSED ============================================================== diffing test.rst7.6.save with test.rst7.6 PASSED ============================================================== diffing test.rst7.7.save with test.rst7.7 PASSED ============================================================== diffing test.rst7.8.save with test.rst7.8 PASSED ============================================================== CPPTRAJ: Trajout Frame Range [Amber Coordinates] diffing framerange.crd.save with framerange.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. diffing PerResRMSD.agr.save with PerResRMSD.agr PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with averaging diffing perresavg.dat.save with perresavg.dat PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with residue centering. diffing center.agr.save with center.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. diffing dssp.gnu.save with dssp.gnu PASSED ============================================================== diffing dssp.sum.agr.save with dssp.sum.agr PASSED ============================================================== diffing total.agr.save with total.agr PASSED ============================================================== diffing DSSP.assign.dat.save with DSSP.assign.dat PASSED ============================================================== CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. diffing dssp.dat.save with dssp.dat PASSED ============================================================== diffing dssp.dat.sum.save with dssp.dat.sum PASSED ============================================================== CPPTRAJ: Secstruct (DSSP) command with changing number of residues. diffing dssp2.gnu.save with dssp2.gnu PASSED ============================================================== diffing dssp2.sum.agr.save with dssp2.sum.agr PASSED ============================================================== CPPTRAJ: Secstruct (DSSP): SS assign output test diffing assign.4.dat.save with assign.4.dat PASSED ============================================================== CPPTRAJ: FtuFabI Assignment test diffing ftufabi.assign.dat.save with ftufabi.assign.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Center CPPTRAJ: Center command test. diffing centered.crd.save with centered.crd PASSED ============================================================== CPPTRAJ: Center origin command test. diffing origin.centered.crd.save with origin.centered.crd PASSED ============================================================== CPPTRAJ: Center origin mass command test. diffing origin.mass.centered.crd.save with origin.mass.centered.crd PASSED ============================================================== CPPTRAJ: Center reference command test. diffing ref.centered.crd.save with ref.centered.crd PASSED ============================================================== CPPTRAJ: Center point test. diffing point.centered.crd.save with point.centered.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Hbond CPPTRAJ: Solute Hbond test diffing nhb.dat.save with nhb.dat PASSED ============================================================== diffing avghb.dat.save with avghb.dat PASSED ============================================================== diffing nbb.dat.save with nbb.dat PASSED ============================================================== diffing hbavg.dat.save with hbavg.dat PASSED ============================================================== diffing solutehb.agr.save with solutehb.agr PASSED ============================================================== diffing lifehb.gnu.save with lifehb.gnu PASSED ============================================================== diffing avg.lifehb.gnu.save with avg.lifehb.gnu PASSED ============================================================== diffing max.lifehb.gnu.save with max.lifehb.gnu PASSED ============================================================== diffing crv.lifehb.gnu.save with crv.lifehb.gnu PASSED ============================================================== CPPTRAJ: Solute Hbond test with disk caching diffing solutehb.agr.save with solutehb2.agr PASSED ============================================================== CPPTRAJ: Solute-solvent hbond test diffing solvhb.dat.save with solvhb.dat PASSED ============================================================== diffing solvavg.dat.save with solvavg.dat PASSED ============================================================== CPPTRAJ: Hbond, no intramolecular hydrogen bonds test diffing hbond.mol.dat.save with hbond.mol.dat PASSED ============================================================== diffing mol.avg.dat.save with mol.avg.dat PASSED ============================================================== CPPTRAJ: Hbond, specified solute masks diffing ud.dat.save with ud.dat PASSED ============================================================== diffing uh.dat.save with uh.dat PASSED ============================================================== diffing ua.dat.save with ua.dat PASSED ============================================================== CPPTRAJ: Hbond, no angle cutoff test diffing noacut.dat.save with noacut.dat PASSED ============================================================== CPPTRAJ: Hbond, Bridge nointramol test diffing bridgeintermol.dat.save with bridgeintermol.dat PASSED ============================================================== diffing avgbridgeintermol.dat.save with avgbridgeintermol.dat PASSED ============================================================== CPPTRAJ: Hbond with imaging diffing hb1.dat.save with hb1.dat PASSED ============================================================== diffing hb2.dat.save with hb2.dat PASSED ============================================================== CPPTRAJ: Hbond, orthogonal imaging diffing solvavg.dat.save with orthoavg.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Hbond_Split CPPTRAJ: Solute Hbond test with split diffing avghb.dat.save with avghb.dat PASSED ============================================================== CPPTRAJ: Solute-solvent hbond test with split diffing solvavg.dat.save with solvavg.dat PASSED ============================================================== diffing bridges.dat.save with bridges.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: NetCDF Restart Test - NetCDF->TXT diffing ../tz2.rst7 with text.rst7 PASSED ============================================================== CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt diffing ../tz2.ortho.rst7 with text.rst7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Image CPPTRAJ: Orthorhombic imaged distance test. diffing ortho.dat.save with ortho.dat PASSED ============================================================== CPPTRAJ: Non-orthorhombic imaged distance test. diffing nonortho.dat.save with nonortho.dat PASSED ============================================================== CPPTRAJ: Orthorhombic coordinate imaging test diffing image.crd.save with image.crd PASSED ============================================================== CPPTRAJ: Nonorthorhombic coordinate imaging test diffing image2.crd.save with image2.crd PASSED ============================================================== CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar diffing image3.crd.save with image3.crd PASSED ============================================================== CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM diffing image4.crd.save with image4.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Surf CPPTRAJ: Surface calculation test diffing surf.dat.save with surf.dat PASSED ============================================================== CPPTRAJ: Partial Surface calculation test diffing tsurf.dat.save with tsurf.dat PASSED ============================================================== CPPTRAJ: LCPO test with GAFF atom types diffing ral.surf.dat.save with ral.surf.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Radgyr CPPTRAJ: Radius of gyration command test diffing radgyr.dat.save with radgyr.dat PASSED ============================================================== diffing radgyr.mass.dat.save with radgyr.mass.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Mask CPPTRAJ: Mask single frame test diffing mask.out.save with mask.out PASSED ============================================================== diffing mask.pdb.1.save with mask.pdb.1 PASSED ============================================================== diffing mask.mol2.1.save with mask.mol2.1 PASSED ============================================================== CPPTRAJ: Mask longer command test. diffing M.dat.save with M.dat PASSED ============================================================== diffing Nselected.dat.save with Nselected.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test diffing Jcoupling.dat.save with Jcoupling.dat PASSED ============================================================== CPPTRAJ: J-Coupling extended test. diffing jc.dat.save with jc.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. diffing noimage.dat.save with noimage.dat PASSED ============================================================== diffing noimage.agr.save with noimage.agr PASSED ============================================================== CPPTRAJ: Diffusion test, old syntax. diffing diff_a.xmgr.save with diff_a.xmgr PASSED ============================================================== diffing diff_r.xmgr.save with diff_r.xmgr PASSED ============================================================== diffing diff_x.xmgr.save with diff_x.xmgr PASSED ============================================================== diffing diff_y.xmgr.save with diff_y.xmgr PASSED ============================================================== diffing diff_z.xmgr.save with diff_z.xmgr PASSED ============================================================== CPPTRAJ: Diffusion test, new syntax. diffing WAT_O.agr.save with WAT_O.agr PASSED ============================================================== diffing DC.dat.save with DC.dat PASSED ============================================================== CPPTRAJ: Diffusion test, nonorthogonal box diffing Nonortho.dat.save with Nonortho.dat PASSED ============================================================== diffing Nonortho.agr.save with Nonortho.agr PASSED ============================================================== CPPTRAJ: STFC Diffusion Test diffing diff.dat.save with diff.dat PASSED ============================================================== CPPTRAJ: STFC Diffusion Test with individual distances diffing diff.1.dat.save with diff.1.dat PASSED ============================================================== CPPTRAJ: STFC Diffusion Test with COM diffing diff.2.dat.save with diff.2.dat PASSED ============================================================== CPPTRAJ: STFC Diffusion Test with second mask diffing diff.3.dat.save with diff.3.dat PASSED ============================================================== diffing nw.dat.save with nw.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing T1.crd with T2.crd PASSED ============================================================== diffing ../tz2.truncoct.crd with test.crd PASSED ============================================================== CPPTRAJ: Outtraj Test with maxmin. diffing maxmin.crd.save with maxmin.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Charmm CPPTRAJ: CHARMM PSF/DCD test diffing test.ala3.pdb.save with test.ala3.pdb.1 PASSED ============================================================== CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: CHARMM DCD Write, step 2. diffing first.ala3.crd with second.ala3.crd PASSED ============================================================== CPPTRAJ: CHAMBER topology read/strip test. diffing strip.chamber.parm7.save with strip.chamber.parm7 PASSED ============================================================== CPPTRAJ: Read CHARMM restart diffing run0.res_0.mol2.save with run0.res_0.mol2 PASSED ============================================================== CPPTRAJ: CHARMM PSF write diffing cpptraj.psf.save with cpptraj.psf PASSED ============================================================== CPPTRAJ: CHARMM COORdinates test diffing cpptraj.cor.save with cpptraj.cor PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) diffing test3.parm7.save with test3.parm7 PASSED ============================================================== diffing testdata.prm.save with testdata.prm PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Rotdif CPPTRAJ: Rotational diffusion calculation test diffing rvecs.dat.save with rvecs.dat PASSED ============================================================== diffing matrices.dat.save with matrices.dat PASSED ============================================================== diffing deffs.dat.save with deffs.dat PASSED ============================================================== diffing rotdif.out.save with rotdif.out PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Convert NetCDF -> mdcrd diffing ../tz2.truncoct.crd with trajectory_test.mdcrd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. diffing R1.dat.save with R1.dat PASSED ============================================================== CPPTRAJ: Coordinate Running Average Traj Write diffing runavg.crd.save with runavg.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_RMSD CPPTRAJ: Basic RMSD tests diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== diffing vecs.dat.save with vecs.dat PASSED ============================================================== diffing rmsd.reftraj.dat.save with rmsd.reftraj.dat PASSED ============================================================== diffing rmsd.reftraj.dat.save with rmsd.refcoords.dat PASSED ============================================================== CPPTRAJ: RMS coordinate rotation/rotation matrices test diffing tz2.norotate.crd.save with tz2.norotate.crd PASSED ============================================================== diffing tz2.rotate.crd.save with tz2.rotate.crd PASSED ============================================================== diffing rmatrices.dat.save with rmatrices.dat PASSED ============================================================== CPPTRAJ: RMS fit with no coordinates modification test. diffing NoMod.dat.save with NoMod.dat PASSED ============================================================== diffing NoMod.crd.save with NoMod.crd PASSED ============================================================== CPPTRAJ: RMS fit to previous test diffing Previous.dat.save with Previous.dat PASSED ============================================================== CPPTRAJ: RMS: imaging after unit cell rotation diffing distances.agr.save with distances.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. diffing rmsd.dat.save with rmsd2.dat PASSED ============================================================== CPPTRAJ: 2D RMSD Test, mass-weighted. diffing rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== CPPTRAJ: 2D RMSD Test with reference trajectory diffing rmsd.dat.save with rmsd1.dat PASSED ============================================================== CPPTRAJ: 2D DME Test. diffing dme.dat.save with dme.dat PASSED ============================================================== CPPTRAJ: 2D RMSD with reference mask test. diffing trp.dat.save with trp.dat PASSED ============================================================== CPPTRAJ: 2D RMSD test, no fitting. diffing nofit.dat.save with nofit.dat PASSED ============================================================== CPPTRAJ: 2D RMSD test, read coords with velocity info diffing rgacc.dat.save with rgacc.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. diffing L01.mol2.1.save with L01.mol2 PASSED ============================================================== diffing tz2.mol2.1.save with tz2.mol2 PASSED ============================================================== CPPTRAJ: PDB => Mol2 diffing test.mol2.save with test.mol2 PASSED ============================================================== CPPTRAJ: Amber Top/Rst => Mol2 diffing test1.mol2.save with test1.mol2 PASSED ============================================================== CPPTRAJ: Amber Top/Rst => Mol2, SYBYL atom types diffing test2.mol2.save with test2.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_NAstruct CPPTRAJ: NAstruct command test. diffing BP.adh026.dat.save with BP.adh026.dat PASSED ============================================================== diffing BPstep.adh026.dat.save with BPstep.adh026.dat PASSED ============================================================== diffing Helix.adh026.dat.save with Helix.adh026.dat PASSED ============================================================== diffing BP.adh026.dat.save with BP.baseref.dat PASSED ============================================================== diffing BPstep.adh026.dat.save with BPstep.baseref.dat PASSED ============================================================== diffing Helix.adh026.dat.save with Helix.baseref.dat PASSED ============================================================== diffing BPstep.groove.dat.save with BPstep.groove.dat PASSED ============================================================== diffing BP.adh026.dat.save with BP.GuessBP.dat PASSED ============================================================== diffing BPstep.adh026.dat.save with BPstep.GuessBP.dat PASSED ============================================================== diffing Helix.adh026.dat.save with Helix.GuessBP.dat PASSED ============================================================== CPPTRAJ: NAstruct command test, single strand diffing SS.mol1.dat.save with SS.mol1.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_NAstruct_8OG CPPTRAJ: NA test (8OG) diffing BP.nastruct.dat.save with BP.nastruct.dat PASSED ============================================================== diffing BPstep.nastruct.dat.save with BPstep.nastruct.dat PASSED ============================================================== diffing Helix.nastruct.dat.save with Helix.nastruct.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Average CPPTRAJ: Average Test. diffing test.pdb.save with test.pdb PASSED ============================================================== diffing test.pdb.save with test2.pdb PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Pucker CPPTRAJ: Pucker command test diffing pucker.dat.save with pucker.dat PASSED ============================================================== CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test diffing CremerF.dat.save with CremerF.dat PASSED ============================================================== CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. diffing CremerP.dat.save with CremerP.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AtomMap CPPTRAJ: AtomMap Test diffing initial.mol2.save with initial.mol2 PASSED ============================================================== diffing atommap.dat.save with atommap.dat PASSED ============================================================== diffing reordered.pdb.save with reordered.pdb PASSED ============================================================== diffing reordered.mol2.save with reordered.mol2 PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing fit.mol2.save with fit.mol2 PASSED ============================================================== CPPTRAJ: AtomMap with 'rmsfit' diffing rmsd.dat.save with rmsout.dat PASSED ============================================================== CPPTRAJ: Atom map charmm->amber atom order diffing map.chm_to_amb.dat.save with map.chm_to_amb.dat PASSED ============================================================== CPPTRAJ: Atom map charmm->amber atom order, by residue diffing map.chm_to_amb.dat.save with map.byres.chm_to_amb.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Datafile CPPTRAJ: Data file output precision test diffing prec.dat.save with prec.dat PASSED ============================================================== CPPTRAJ: Standard -> Grace Data CPPTRAJ: Grace -> Standard Data diffing ../Test_General/a1.dat.save with a1.dat PASSED ============================================================== CPPTRAJ: X column format/precision test. diffing xprec.dat.save with xprec.dat PASSED ============================================================== CPPTRAJ: Data file group by name test diffing byname.dat.save with byname.dat PASSED ============================================================== CPPTRAJ: Data file group by aspect test diffing dssp.dat.save with dssp.dat PASSED ============================================================== diffing byidx.dat.save with byidx.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Radial CPPTRAJ: Radial test, non-orthogonal imaging diffing Radial.agr.save with Radial.agr PASSED ============================================================== diffing cRadial.agr.save with cRadial.agr PASSED ============================================================== diffing WatO-Trp4.agr.save with WatO-Trp4.agr PASSED ============================================================== diffing WatO-Trp4.raw.agr.save with WatO-Trp4.raw.agr PASSED ============================================================== diffing WatO-Trp4.agr.save with WatO-Trp4.byres.agr PASSED ============================================================== diffing WatO-Trp.agr.save with WatO-Trp.agr PASSED ============================================================== diffing WatO-Trp.volume.agr.save with WatO-Trp.volume.agr PASSED ============================================================== CPPTRAJ: Radial test, orthogonal and no imaging diffing WatO-Glu5CD.agr.save with WatO-Glu5CD.agr PASSED ============================================================== diffing noimage.WatO-Glu5CD.agr.save with noimage.WatO-Glu5CD.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Hist CPPTRAJ: 1D/2D Histogram Analysis test diffing hist.gnu.save with hist.gnu PASSED ============================================================== diffing hist.agr.save with hist.agr PASSED ============================================================== diffing freeE.gnu.save with freeE.gnu PASSED ============================================================== diffing norm.gnu.save with norm.gnu PASSED ============================================================== diffing phipsihist.agr.save with phipsihist.agr PASSED ============================================================== diffing phipsikde.agr.save with phipsikde.agr PASSED ============================================================== CPPTRAJ: 3D histogram test. diffing hist.dx.save with hist.dx PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Closest CPPTRAJ: Closest command test using first solvent atom. diffing first.Closest.pdb.save with first.Closest.pdb.1 PASSED ============================================================== diffing closestmols.dat.save with closestmols.dat PASSED ============================================================== diffing closest.tz2.truncoct.parm7.save with closest.tz2.truncoct.parm7 PASSED ============================================================== CPPTRAJ: Closest command test using all solvent atoms. diffing all.Closest.pdb.save with all.Closest.pdb.1 PASSED ============================================================== CPPTRAJ: Closest command test, using mask center diffing closest10.center2_4.crd.save with closest10.center2_4.crd PASSED ============================================================== diffing closest10.mols.dat.save with closest10.mols.dat PASSED ============================================================== CPPTRAJ: Closest command test, using mask center and solvent mask diffing closest10.mols.dat.save with solventmask.dat PASSED ============================================================== CPPTRAJ: Closest command test, solvent mask, water oxygen only diffing wato.dat.save with wato.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_DRMSD CPPTRAJ: Distance RMSD test diffing drmsd.dat.save with drmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster CPPTRAJ: Cluster command test, in-memory pairwise distances. diffing cnumvtime.dat.save with cnumvtime.dat PASSED ============================================================== diffing cinfo.dat.save with cinfo.dat PASSED ============================================================== diffing mysil.cluster.dat.save with mysil.cluster.dat PASSED ============================================================== diffing mysil.frame.dat.save with mysil.frame.dat PASSED ============================================================== diffing avg.summary.dat.save with avg.summary.dat PASSED ============================================================== diffing c1.cmetrics.dat.save with c1.cmetrics.dat PASSED ============================================================== diffing summary.dat.save with summary.dat PASSED ============================================================== diffing cpop.agr.save with cpop.agr PASSED ============================================================== CPPTRAJ: Cluster command test, read pairwise distances. diffing summary.dat.save with summary2.dat PASSED ============================================================== diffing normpop.agr.save with normpop.agr PASSED ============================================================== CPPTRAJ: Cluster command test, read NetCDF pairwise distances. diffing summary.dat.save with summary3.dat PASSED ============================================================== diffing normframe.agr.save with normframe.agr PASSED ============================================================== CPPTRAJ: Cluster command test, write ASCII pairwise distances. CPPTRAJ: Cluster command test, read ASCII pairwise distances, use cached frames. diffing cascii.dat.save with cascii.dat PASSED ============================================================== diffing cascii1.info with cascii2.info PASSED ============================================================== CPPTRAJ: Cluster command test, read ASCII pairwise distances. diffing cascii.dat.save with cascii.dat PASSED ============================================================== diffing cascii1.info with cascii3.info PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5 diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve savepairdist diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve loadpairdist diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5 savepairdist diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== diffing sieve5.nc.c0.save with sieve5.nc.c0 PASSED ============================================================== CPPTRAJ: Cluster, sieve5 loadpairdist diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve pairwisecache none diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5 pairwisecache none diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, random diffing random.info.dat.save with random.info.dat PASSED ============================================================== diffing random.half.dat.save with random.half.dat PASSED ============================================================== diffing random.sil.cluster.dat.save with random.sil.cluster.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). diffing random.info.dat.save with random.info.dat PASSED ============================================================== diffing random.summary.dat.save with random.summary.dat PASSED ============================================================== CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). diffing random.info.dat.save with random.info.dat PASSED ============================================================== diffing random.summary.dat.save with random.summary.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_DataSet CPPTRAJ: Clustering, One DataSet diffing oneds.info.dat.save with oneds.info.dat PASSED ============================================================== diffing eps_v_n.dat.save with eps_v_n.dat PASSED ============================================================== diffing cvt.dat.save with cvt.dat PASSED ============================================================== CPPTRAJ: Clustering, Two DataSets diffing twods.info.dat.save with twods.info.dat PASSED ============================================================== diffing twods.metricstats.save with twods.metricstats PASSED ============================================================== CPPTRAJ: Clustering, Two DataSets, Manhattan distance diffing twodsm.info.dat.save with twodsm.info.dat PASSED ============================================================== diffing twodsm.metricstats.save with twodsm.metricstats PASSED ============================================================== CPPTRAJ: Clustering, Two DataSets with specified weights diffing twodswgt.info.dat.save with twodswgt.info.dat PASSED ============================================================== diffing twodswgt.metricstats.save with twodswgt.metricstats PASSED ============================================================== CPPTRAJ: Clustering, dihedral DataSet diffing onedihds.info.dat.save with onedihds.info.dat PASSED ============================================================== CPPTRAJ: Clustering, two dihedral DataSets diffing twodihds.info.dat.save with twodihds.info.dat PASSED ============================================================== CPPTRAJ: Clustering, dihedral DataSet, K-means diffing onedihds.kmeans.info.dat.save with onedihds.kmeans.info.dat PASSED ============================================================== CPPTRAJ: Clustering, two dihedral DataSets, K-means diffing twodihds.kmeans.info.dat.save with twodihds.kmeans.info.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test diffing rvc.dat.save with rvc.dat PASSED ============================================================== diffing info.dat.save with info.dat PASSED ============================================================== CPPTRAJ: DBSCAN automatic parameter determination test. diffing Kdist.dat.save with Kdist.4.dat PASSED ============================================================== CPPTRAJ: DBSCAN kdist map test diffing Kmatrix.gnu.save with Kmatrix.gnu PASSED ============================================================== CPPTRAJ: DBSCAN with sieve diffing sieveinfo.dat.2.save with sieveinfo.dat.2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans diffing summary.dat.save with summary.dat PASSED ============================================================== diffing info.dat.save with info.dat PASSED ============================================================== diffing cpptraj.crd.c0.save with cpptraj.crd.c0 PASSED ============================================================== CPPTRAJ: Cpptraj Kmeans random diffing random.dat.save with random.dat PASSED ============================================================== diffing info.dat.save with rinfo.dat PASSED ============================================================== diffing cpptraj.crd.c0.save with random.crd.c0 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) diffing rms.summary.dat.save with rms.summary.dat PASSED ============================================================== diffing rms.info.dat.save with rms.info.dat PASSED ============================================================== diffing srmsd.summary.dat.save with srmsd.summary.dat PASSED ============================================================== diffing srmsd.info.dat.save with srmsd.info.dat PASSED ============================================================== diffing 2drms.gnu.save with 2drms.gnu PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: Cluster command test, coordinate writes using info file. diffing clusterinfo.txt.save with clusterinfo.txt PASSED ============================================================== diffing cluster.c0.save with cluster.c0 PASSED ============================================================== diffing rep.1.crd.save with rep.c8.1.crd PASSED ============================================================== diffing single.save with single PASSED ============================================================== diffing avg.summary.dat.save with avg.summary.dat PASSED ============================================================== diffing lifetime.dat.save with lifetime.dat PASSED ============================================================== diffing Avg.c0.rst7.save with Avg.c0.rst7 PASSED ============================================================== diffing cluster.c0.save with fromInfo.c0 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test diffing dpeaks.dat.save with dpeaks.dat PASSED ============================================================== diffing summary.dat.save with summary.dat PASSED ============================================================== diffing info.dat.save with info.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_Nreps CPPTRAJ: Cluster representative frames tests diffing clusters.2.dat.save with clusters.2.dat PASSED ============================================================== diffing summary.2.dat.save with summary.2.dat PASSED ============================================================== CPPTRAJ: Test cumulative best rep diffing cumulative.save with cumulative PASSED ============================================================== CPPTRAJ: Test centroid best rep diffing centroid.save with centroid PASSED ============================================================== CPPTRAJ: Test cumulative, no sieve best rep diffing cumulative_nosieve.save with cumulative_nosieve PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_AssignRefs CPPTRAJ: Clustering, assign reference names diffing ksummary.dat.save with ksummary.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_Cache CPPTRAJ: Cluster, nosieve.mem.save savepairdist pairdist PW0 pairwisecache mem CPPTRAJ: Cluster, nosieve.mem.load loadpairdist pairdist PW0 diffing nosieve.mem.save.info.dat.save with nosieve.mem.save.info.dat PASSED ============================================================== diffing nosieve.mem.save.cnumvtime.dat with nosieve.mem.load.cnumvtime.dat PASSED ============================================================== diffing nosieve.mem.save.info.dat with nosieve.mem.load.info.dat PASSED ============================================================== diffing nosieve.mem.save.summary.dat with nosieve.mem.load.summary.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve.disk.save savepairdist pairdist PW1 pairwisecache disk diffing nosieve.mem.save.info.dat.save with nosieve.disk.save.info.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve.disk.load loadpairdist pairdist PW1 diffing nosieve.mem.save.info.dat.save with nosieve.disk.load.info.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve.nocache.save pairwisecache none diffing nosieve.mem.save.info.dat.save with nosieve.nocache.save.info.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5.mem.save savepairdist pairdist PW0 pairwisecache mem CPPTRAJ: Cluster, sieve5.mem.load loadpairdist pairdist PW0 diffing sieve5.mem.save.info.dat.save with sieve5.mem.save.info.dat PASSED ============================================================== diffing sieve5.mem.save.cnumvtime.dat with sieve5.mem.load.cnumvtime.dat PASSED ============================================================== diffing sieve5.mem.save.info.dat with sieve5.mem.load.info.dat PASSED ============================================================== diffing sieve5.mem.save.summary.dat with sieve5.mem.load.summary.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5.disk.save savepairdist pairdist PW1 pairwisecache disk diffing sieve5.mem.save.info.dat.save with sieve5.disk.save.info.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5.nocache.save pairwisecache none diffing sieve5.mem.save.info.dat.save with sieve5.nocache.save.info.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve3.mem.load loadpairdist pairdist PW1 pwrecalc diffing sieve3.mem.load.info.dat.save with sieve3.mem.load.info.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_ReadInfo CPPTRAJ: Hierarchical aggolmerative cluster restart test, part 1 CPPTRAJ: Hierarchical agglomerative cluster restart test, part 2 diffing C1.info.dat with C3.info.dat PASSED ============================================================== diffing C1.info.dat with C10.info.dat PASSED ============================================================== CPPTRAJ: K-means cluster restart test, part 1 CPPTRAJ: K-means cluster restart test, part 2 diffing C4.info.dat with C6.info.dat PASSED ============================================================== CPPTRAJ: K-means cluster restart, 3 to 8 clusters. diffing C7.info.dat.save with C7.info.dat PASSED ============================================================== CPPTRAJ: DBscan cluster restart, part 1 CPPTRAJ: DBscan cluster restart, part 2 diffing C9.info.dat.save with C9.info.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cluster_CoordsAndData CPPTRAJ: Test clustering on coordinates and data diffing c1.info.dat.save with c1.info.dat PASSED ============================================================== diffing c1.summary.dat.save with c1.summary.dat PASSED ============================================================== diffing c1.cnvt.dat.save with c1.cnvt.dat PASSED ============================================================== diffing metricstats.dat.save with metricstats.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_IRED CPPTRAJ: IRED vector/matrix test diffing ired.vec.save with ired.vec PASSED ============================================================== diffing v0.cmt.new.norm.save with v0.cmt PASSED ============================================================== diffing plateau.norm.dat.save with plateau.norm.dat PASSED ============================================================== diffing v0.cjt.new.save with v0.cjt PASSED ============================================================== diffing orderparam.save with orderparam PASSED ============================================================== diffing matrix_ds2.dat.save with matrix_ds2.dat PASSED ============================================================== diffing noe.save with noe PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_RandomizeIons CPPTRAJ: randomizeions test (original algorithm) diffing random.crd.save with random.crd PASSED ============================================================== CPPTRAJ: Randomize (around, overlap) diffing around.overlap.rst7.save with around.overlap.rst7 PASSED ============================================================== CPPTRAJ: Randomize (around) diffing around.rst7.save with around.rst7 PASSED ============================================================== CPPTRAJ: Randomize (overlap) diffing overlap.rst7.save with overlap.rst7 PASSED ============================================================== CPPTRAJ: Randomize (no restrictions) diffing norestrict.rst7.save with norestrict.rst7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Molsurf CPPTRAJ: Molsurf test diffing msurf.dat.save with msurf.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Corr CPPTRAJ: Correlation test diffing corr.dat.save with corr.dat PASSED ============================================================== diffing cross.dat.save with cross.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CheckStructure CPPTRAJ: Structure Check diffing report.dat.save with report.dat PASSED ============================================================== diffing report.dat.save with partial.report.dat PASSED ============================================================== diffing nprob.dat.save with nprob.dat PASSED ============================================================== CPPTRAJ: Structure Check with Around and Skip diffing skip.dat.save with skip.dat PASSED ============================================================== diffing d1.dat.save with d1.dat PASSED ============================================================== CPPTRAJ: Structure Check with PBC diffing tz2.dat.save with tz2.dat PASSED ============================================================== diffing tz2.cut0.9.dat.save with tz2.cut0.9.dat PASSED ============================================================== CPPTRAJ: Structure Check with Around diffing around.dat.save with around.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference diffing rmscorr.dat.save with rmscorr.dat PASSED ============================================================== diffing rmscorr.10.dat.save with rmscorr.10.dat PASSED ============================================================== CPPTRAJ: RmsAvgCorr First diffing rmscorr.first.dat.save with rmscorr.first.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Contacts CPPTRAJ: Contacts test. diffing contacts.dat.save with contacts.dat PASSED ============================================================== diffing byres.dat.save with byres.dat PASSED ============================================================== diffing byres.dat.native.save with byres.dat.native PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Principal CPPTRAJ: Principal Test diffing Ctest.crd.save with Ctest.crd PASSED ============================================================== diffing principal.dat.save with principal.dat PASSED ============================================================== diffing eigen.dat.save with eigen.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_ClusterDihedral CPPTRAJ: clusterdihedral test diffing cd.dat.save with cd.dat PASSED ============================================================== diffing cf.dat.save with cf.dat PASSED ============================================================== diffing ci.dat.save with ci.dat PASSED ============================================================== diffing cvt.dat.save with cvt.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Vector CPPTRAJ: Basic vector tests diffing vtest.dat.0.save with vtest.dat.0 PASSED ============================================================== diffing vtest.dat.1.save with vtest.dat.1 PASSED ============================================================== diffing vtest.dat.2.save with vtest.dat.2 PASSED ============================================================== diffing vtest.dat.3.save with vtest.dat.3 PASSED ============================================================== diffing vtest.dat.4.save with vtest.dat.4 PASSED ============================================================== diffing vtest.dat.5.save with vtest.dat.5 PASSED ============================================================== diffing vtest.dat.6.save with vtest.dat.6 PASSED ============================================================== diffing vtest.dat.7.save with vtest.dat.7 PASSED ============================================================== diffing v8.mol2.save with v8.mol2 PASSED ============================================================== CPPTRAJ: Test vector center with magnitude diffing avgcoord.out.save with avgcoord.out PASSED ============================================================== diffing res5.out.save with res5.out PASSED ============================================================== CPPTRAJ: Momentum/velocity vector test. diffing vtest.dat.9.save with vtest.dat.9 PASSED ============================================================== diffing vtest.dat.10.save with vtest.dat.10 PASSED ============================================================== CPPTRAJ: Force vector test. diffing vtest.dat.11.save with vtest.dat.11 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Matrix CPPTRAJ: Matrix Tests diffing mtest.dat.0.save with mtest.0.dat PASSED ============================================================== diffing mtest.dat.1.save with mtest.1.dat PASSED ============================================================== diffing mtest.dat.2.save with mtest.2.dat PASSED ============================================================== diffing mtest.dat.3.save with mtest.3.dat PASSED ============================================================== diffing mtest.dat.4.save with mtest.4.dat PASSED ============================================================== diffing mtest.dat.5.save with mtest.5.dat PASSED ============================================================== diffing mtest.dat.6.save with mtest.6.dat PASSED ============================================================== diffing mtest.dat.7.save with mtest.7.dat PASSED ============================================================== diffing mtest.dat.8.save with mtest.8.dat PASSED ============================================================== diffing mtest.dat.9.save with mtest.9.dat PASSED ============================================================== diffing mtest.dat.10.save with mtest.10.dat PASSED ============================================================== diffing mtest.dat.11.save with mtest.11.dat PASSED ============================================================== diffing mtest.dat.12.save with mtest.12.dat PASSED ============================================================== diffing mtest.dat.13.save with mtest.13.dat PASSED ============================================================== CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: Generate matrix with action stop/start/offset diffing tz2.dist.ca.matrix.dat.save with tz2.dist.ca.matrix.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. diffing fluct.1.dat.save with fluct.1.dat PASSED ============================================================== CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. diffing fluct.2.dat.save with fluct.2.dat PASSED ============================================================== CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. diffing fluct.3.dat.save with fluct.3.dat PASSED ============================================================== CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. diffing fluct.4.dat.save with fluct.4.dat PASSED ============================================================== CPPTRAJ: Atomicfluct test with ADP output diffing dpdp.fluct.dat.save with dpdp.fluct.dat PASSED ============================================================== diffing dpdp.adp.dat.save with dpdp.adp.dat PASSED ============================================================== diffing dpdp.adp.pdb.save with dpdp.adp.pdb PASSED ============================================================== diffing myfluct.adp.dat.save with myfluct.adp.dat PASSED ============================================================== diffing heavy.adp.pdb.save with heavy.adp.pdb PASSED ============================================================== CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. diffing fluct.2.pdb.save with fluct.2.pdb PASSED ============================================================== diffing occ.2.pdb.save with occ.2.pdb PASSED ============================================================== diffing scale.2.pdb.save with scale.2.pdb PASSED ============================================================== diffing fluct.1.pdb.save with fluct.1.pdb PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Grid CPPTRAJ: Dipole test diffing out.dipole.save with out.dipole PASSED ============================================================== CPPTRAJ: Grid test diffing out.xplor.save with out.xplor PASSED ============================================================== diffing out.dx.save with out.dx PASSED ============================================================== diffing byres.dx.save with byres.dx PASSED ============================================================== diffing byres.dx.save with bymol.dx PASSED ============================================================== CPPTRAJ: OpenDX Grid read test diffing out.dx.2.save with out.dx.2 PASSED ============================================================== CPPTRAJ: Grid with specified center test. diffing test.dx.save with test.dx PASSED ============================================================== CPPTRAJ: Grid with box center offset test. diffing box.dx.save with box.dx PASSED ============================================================== CPPTRAJ: Grid with mask center offset test. diffing mask.dx.save with mask.dx PASSED ============================================================== CPPTRAJ: Non-orthogonal grid test. diffing nonortho.dx.save with nonortho.dx PASSED ============================================================== CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test diffing nonortho_wrap.dx.save with nonortho_wrap.dx PASSED ============================================================== CPPTRAJ: Grid generation from 'bounds' test. diffing bounds.dat.save with bounds.dat PASSED ============================================================== diffing bounds.xplor.save with bounds.xplor PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Grid_Rotate_Simple CPPTRAJ: RMS-fitting grid test diffing tyr.gridfit.dx.save with tyr.gridfit.dx PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Unwrap CPPTRAJ: Unwrap non-orthogonal test diffing unwrap.crd.save with unwrap.crd PASSED ============================================================== CPPTRAJ: Unwrap orthogonal test diffing unwrap.ortho.crd.save with unwrap.ortho.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Project CPPTRAJ: Projection diffing project.dat.save with project.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations diffing fluct.dat.save with fluct.dat PASSED ============================================================== CPPTRAJ: Modes analysis, displacements diffing displ.dat.save with displ.dat PASSED ============================================================== CPPTRAJ: Modes analysis, dipole correlation diffing corr.dat.save with corr.dat PASSED ============================================================== CPPTRAJ: Modes analysis, pseudo trajectory creation test diffing modestest.2.crd.save with modestest.2.crd PASSED ============================================================== CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test diffing rmsip.dat.save with rmsip.dat PASSED ============================================================== diffing eigenval.dat.save with eigenval.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Watershell CPPTRAJ: Watershell Test, non-orthorhombic imaging. diffing ws.agr.save with ws.agr PASSED ============================================================== CPPTRAJ: Watershell Test, orthorhombic imaging. diffing ws.ortho.agr.save with ws.ortho.agr PASSED ============================================================== CPPTRAJ: Watershell Test, no imaging. diffing ws.noimage.agr.save with ws.noimage.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average diffing running_avg.dat.save with running_avg.dat PASSED ============================================================== diffing cumulative_avg.dat.save with cumulative_avg.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Volmap CPPTRAJ: VMD VolMap Algorithm test diffing volmap3.dx.save with volmap3.dx PASSED ============================================================== diffing peaks1.xyz.save with peaks1.xyz PASSED ============================================================== VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_SPAM CPPTRAJ: SPAM Test diffing summary.dat.save with summary.dat PASSED ============================================================== diffing test.mdcrd.save with test.mdcrd PASSED ============================================================== diffing spam.info.save with spam.info PASSED ============================================================== diffing spam.dat.save with spam.dat PASSED ============================================================== CPPTRAJ: SPAM Pure Solvent Test diffing spampure.dat.save with spampure.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LIE CPPTRAJ: LIE test diffing TCL.out.save with TCL.out PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Density CPPTRAJ: Density along axis tests diffing number_density.dat.save with number_density.dat PASSED ============================================================== diffing mass_density.dat.save with mass_density.dat PASSED ============================================================== diffing charge_density.dat.save with charge_density.dat PASSED ============================================================== diffing electron_density.dat.save with electron_density.dat PASSED ============================================================== CPPTRAJ: Multi-frame density along axis test diffing tz2.wato.agr.save with tz2.wato.agr PASSED ============================================================== diffing restrict.agr.save with restrict.agr PASSED ============================================================== CPPTRAJ: Total system density test diffing total.dat.save with total.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. diffing sn1_est.dat.save with sn1_est.dat PASSED ============================================================== diffing e2e_sn1.dat.save with e2e_sn1.dat PASSED ============================================================== diffing sn2_est.dat.save with sn2_est.dat PASSED ============================================================== diffing e2e_sn2.dat.save with e2e_sn2.dat PASSED ============================================================== diffing sn1_dir.dat.save with sn1_dir.dat PASSED ============================================================== diffing sn2_dir.dat.save with sn2_dir.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LipidSCD CPPTRAJ: Basic lipid order parameter test diffing ol1.dat.save with ol1.dat PASSED ============================================================== diffing ol2.dat.save with ol2.dat PASSED ============================================================== diffing ol3.agr.save with ol3.agr PASSED ============================================================== CPPTRAJ: New Lipid Order Parameter Test, DOPC. diffing dopc.agr.save with dopc.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_PairDist CPPTRAJ: PairDist Test. diffing Pr.dat.save with Pr.dat PASSED ============================================================== CPPTRAJ: Pairdist test, orthogonal imaging. diffing ortho.dat.save with ortho.dat PASSED ============================================================== CPPTRAJ: Pairdist test, nonorthogonal imaging. diffing truncoct.dat.save with truncoct.dat PASSED ============================================================== CPPTRAJ: Pairdist test, 2 masks. diffing twomask.dat.save with twomask.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_ReadData CPPTRAJ: Read vector data test (no origins, origins) diffing v6and7.dat.save with v6and7.dat PASSED ============================================================== CPPTRAJ: Read vector data set (origins, no origins) diffing v7and6.dat.save with v7and6.dat PASSED ============================================================== CPPTRAJ: Read Amber output test diffing MD.ene.dat.save with MD.ene.dat PASSED ============================================================== CPPTRAJ: Read CHARMM output test diffing rex-d.dat.save with rex-d.dat PASSED ============================================================== CPPTRAJ: 3D data read/write test diffing ../Test_Grid/out.dx.save with out.dx PASSED ============================================================== CPPTRAJ: Standard 3D data write test CPPTRAJ: Standard 3D data read test diffing ../Test_Grid/out.dx.save with out2.dx PASSED ============================================================== CPPTRAJ: Standard 3D data read/append test diffing append.dat.save with append.dat PASSED ============================================================== CPPTRAJ: Standard 3D data, sparse diffing ../Test_Grid/out.dx.save with out3.dx PASSED ============================================================== CPPTRAJ: Nonorthogonal grid standard write/read tests. diffing truncsparse.dat.save with truncsparse.dat PASSED ============================================================== diffing truncoct.dat.save with temp.dat PASSED ============================================================== diffing truncoct.dat.save with temp2.dat PASSED ============================================================== CPPTRAJ: Read specific columns test. diffing xyz.dat.save with xyz.dat PASSED ============================================================== CPPTRAJ: Write non-square matrix diffing matrix.dat.save with matrix.dat PASSED ============================================================== CPPTRAJ: Read non-square matrix diffing matrix.dat.save with cpptraj.matrix.dat PASSED ============================================================== CPPTRAJ: Read square matrix diffing ../Test_Matrix/mtest.dat.13.save with square.matrix.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_GIST CPPTRAJ: GIST water-water interaction test diffing Gist1-Eww_ij.dat.save with Gist1-Eww_ij.dat PASSED ============================================================== CPPTRAJ: GIST test, orthogonal cell diffing Gist2-gH.dx.save with Gist2-gH.dx PASSED ============================================================== diffing Gist2-gO.dx.save with Gist2-gO.dx PASSED ============================================================== diffing Gist2-neighbor-norm.dx.save with Gist2-neighbor-norm.dx PASSED ============================================================== diffing Gist2-order-norm.dx.save with Gist2-order-norm.dx PASSED ============================================================== diffing gist.out.save with Gist2-output.dat PASSED ============================================================== CPPTRAJ: GIST test, nonorthogonal cell diffing Gist3-gH.dx.save with Gist3-gH.dx PASSED ============================================================== diffing Gist3-gO.dx.save with Gist3-gO.dx PASSED ============================================================== diffing Gist3-neighbor-norm.dx.save with Gist3-neighbor-norm.dx PASSED ============================================================== diffing Gist3-order-norm.dx.save with Gist3-order-norm.dx PASSED ============================================================== diffing Gist3-output.dat.save with Gist3-output.dat PASSED ============================================================== CPPTRAJ: PME-GIST test on orthogonal cell diffing Gist4-Solute-Etot-pme-dens.dx.save with Gist4-Solute-Etot-pme-dens.dx PASSED ============================================================== diffing Gist4-Water-Etot-pme-dens.dx.save with Gist4-Water-Etot-pme-dens.dx PASSED ============================================================== diffing Gist2-gH.dx.save with Gist4-gH.dx PASSED ============================================================== diffing Gist2-gO.dx.save with Gist4-gO.dx PASSED ============================================================== diffing Gist2-neighbor-norm.dx.save with Gist4-neighbor-norm.dx PASSED ============================================================== diffing Gist4-Esw-dens.dx.save with Gist4-Esw-dens.dx PASSED ============================================================== diffing Gist4-Eww-dens.dx.save with Gist4-Eww-dens.dx PASSED ============================================================== diffing Gist4-Info.dat.save with Gist4-Info.dat PASSED ============================================================== CPPTRAJ: PME-GIST test on non-orthogonal cell diffing Gist5-Solute-Etot-pme-dens.dx.save with Gist5-Solute-Etot-pme-dens.dx PASSED ============================================================== diffing Gist5-Water-Etot-pme-dens.dx.save with Gist5-Water-Etot-pme-dens.dx PASSED ============================================================== diffing Gist3-gH.dx.save with Gist5-gH.dx PASSED ============================================================== diffing Gist3-gO.dx.save with Gist5-gO.dx PASSED ============================================================== diffing Gist3-neighbor-norm.dx.save with Gist5-neighbor-norm.dx PASSED ============================================================== diffing Gist5-Esw-dens.dx.save with Gist5-Esw-dens.dx PASSED ============================================================== diffing Gist5-Eww-dens.dx.save with Gist5-Eww-dens.dx PASSED ============================================================== diffing Gist5-Info.dat.save with Gist5-Info.dat PASSED ============================================================== CPPTRAJ: GIST test, orthogonal cell, oldnnvolume diffing Gist6-gH.dx.save with Gist6-gH.dx PASSED ============================================================== diffing Gist6-gO.dx.save with Gist6-gO.dx PASSED ============================================================== diffing Gist6-neighbor-norm.dx.save with Gist6-neighbor-norm.dx PASSED ============================================================== diffing Gist6-order-norm.dx.save with Gist6-order-norm.dx PASSED ============================================================== diffing Gist6.out.save with Gist6-output.dat PASSED ============================================================== CPPTRAJ: GIST test, orthogonal cell, nnsearchlayers 5 diffing Gist7-gH.dx.save with Gist7-gH.dx PASSED ============================================================== diffing Gist7-gO.dx.save with Gist7-gO.dx PASSED ============================================================== diffing Gist7-neighbor-norm.dx.save with Gist7-neighbor-norm.dx PASSED ============================================================== diffing Gist7-order-norm.dx.save with Gist7-order-norm.dx PASSED ============================================================== diffing Gist7.out.save with Gist7-output.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test diffing gist-order-norm.dx.save with gist-order-norm.dx PASSED ============================================================== diffing gistout.dat.save with gistout.dat PASSED ============================================================== CPPTRAJ: TIP4P water cluster test diffing tip4p.dat.save with tip4p.dat PASSED ============================================================== CPPTRAJ: TIP5P water cluster test diffing tip5p.dat.save with tip5p.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_systemVF CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test diffing systemVF.nc with test.systemVF.nc PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test diffing acorr.gnu.save with acorr.gnu PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AutoCorr CPPTRAJ: AutoCorr test. diffing ac.agr.save with ac.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Box CPPTRAJ: Box Test (Add box info) diffing addbox.rst7.1.save with addbox.rst7.1 PASSED ============================================================== diffing addbox.rst7.10.save with addbox.rst7.10 PASSED ============================================================== CPPTRAJ: Box test (remove box info) diffing frame1.rst7.save with frame1.rst7 PASSED ============================================================== CPPTRAJ: Box test (Modify box length) diffing modX.rst7.1.save with modX.rst7.1 PASSED ============================================================== diffing modX.rst7.10.save with modX.rst7.10 PASSED ============================================================== CPPTRAJ: Box test (auto orthogonal box, no radii) diffing tz2.box.rst7.save with tz2.box.rst7 PASSED ============================================================== CPPTRAJ: Box test (auto orthogonal box, VDW radii) diffing tz2.vdw.rst7.save with tz2.vdw.rst7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. diffing rmsavg.dat.save with rmsavg.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Crank_Stat CPPTRAJ: Crankshaft test diffing crank.dat.save with crank.dat PASSED ============================================================== diffing results.dat.save with results.dat PASSED ============================================================== diffing stat.dat.save with stat.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. diffing crd1.dat.save with crd1.dat PASSED ============================================================== CPPTRAJ: COORDS data set creation with velocities test diffing crd0.rst7 with crd.rst7 PASSED ============================================================== diffing crd1.rst7.save with crd1.rst7 PASSED ============================================================== CPPTRAJ: TRAJ data set creation and CRDFLUCT test. diffing crd1.dat.save with traj1.dat PASSED ============================================================== CPPTRAJ: TRAJ data set creation with velocities test. diffing crd1.rst7.save with crd2.rst7 PASSED ============================================================== CPPTRAJ: COORDS data set append test diffing crd3.dat with crd4.dat PASSED ============================================================== CPPTRAJ: COORDS test storing frame metadata diffing mremd.nc.save with mremd.nc PASSED ============================================================== CPPTRAJ: TRAJ test storing frame metadata diffing ../Test_Ensemble_MREMD/rGACC.nowat.001 with mremd.traj.nc PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) diffing reimage.mdcrd.save with reimage.mdcrd PASSED ============================================================== CPPTRAJ: AutoImage test, use anchor mask diffing image.G3_3A.rst7.save with image.G3_3A.rst7 PASSED ============================================================== CPPTRAJ: AutoImage test, non-sequential molecules diffing image.cpptraj.Fg238.rst7.save with image.cpptraj.Fg238.rst7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LoadCrd CPPTRAJ: LoadCrd test. diffing d1-10.dat.save with d1-10.dat PASSED ============================================================== CPPTRAJ: LoadTraj test. diffing d1-10.dat.save with d1-10.dat PASSED ============================================================== CPPTRAJ: LoadTraj from trajin test. diffing d1-10.dat.save with d1-10.dat PASSED ============================================================== CPPTRAJ: LoadCrd append from multiple files test diffing d1-12.dat.save with d1-12.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_MultiVector CPPTRAJ: Multivector test diffing NH.dat.save with NH.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Lifetime CPPTRAJ: Lifetime test. diffing avg.life.5.gnu.save with avg.life.5.gnu PASSED ============================================================== diffing max.life.5.gnu.save with max.life.5.gnu PASSED ============================================================== diffing life.5.gnu.save with life.5.gnu PASSED ============================================================== diffing crv.life.5.gnu.save with crv.life.5.gnu PASSED ============================================================== diffing solutehb.gnu.save with solutehb.gnu PASSED ============================================================== CPPTRAJ: Lifetime test with data set caching. diffing avg.life.5.gnu.save with avg.life2.5.gnu PASSED ============================================================== diffing max.life.5.gnu.save with max.life2.5.gnu PASSED ============================================================== diffing life.5.gnu.save with life2.5.gnu PASSED ============================================================== diffing crv.life.5.gnu.save with crv.life2.5.gnu PASSED ============================================================== diffing solutehb.gnu.save with solutehb2.gnu PASSED ============================================================== CPPTRAJ: Lifetime average and cumulative average test. diffing perres.avg.gnu.save with perres.avg.gnu PASSED ============================================================== diffing perres.cumulative.gnu.save with perres.cumulative.gnu PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_FFT CPPTRAJ: FFT test. diffing fft.agr.save with fft.agr PASSED ============================================================== diffing fft1.agr.save with fft1.agr PASSED ============================================================== diffing fft2.agr.save with fft2.agr PASSED ============================================================== diffing fft3.agr.save with fft3.agr PASSED ============================================================== diffing fft4.agr.save with fft4.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Timecorr CPPTRAJ: Timecorr test. diffing v1.auto.dat.save with v1.auto.dat PASSED ============================================================== diffing v1v2.cross.dat.save with v1v2.cross.dat PASSED ============================================================== diffing v1.dplr.auto.dat.save with v1.dplr.auto.dat PASSED ============================================================== diffing v1v2.dplr.cross.dat.save with v1v2.dplr.cross.dat PASSED ============================================================== diffing v1.o0.auto.dat.save with v1.o0.auto.dat PASSED ============================================================== diffing v1.o1.auto.dat.save with v1.o1.auto.dat PASSED ============================================================== diffing tz2.2.3.cross.dat.save with tz2.2.3.cross.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CrossCorr CPPTRAJ: CrossCorr test diffing cc.gnu.save with cc.gnu PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_SymmRmsd CPPTRAJ: SymmRmsd diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== CPPTRAJ: ASP symmetry-corrected RMSD test diffing ASP.rmsd.dat.save with ASP.rmsd.dat PASSED ============================================================== diffing ASP.remap.crd.save with ASP.remap.crd PASSED ============================================================== CPPTRAJ: GLU symmetry-corrected RMSD test diffing GLU.rmsd.dat.save with GLU.rmsd.dat PASSED ============================================================== diffing GLU.remap.crd.save with GLU.remap.crd PASSED ============================================================== CPPTRAJ: TYR symmetry-corrected RMSD test diffing TYR.rmsd.dat.save with TYR.rmsd.dat PASSED ============================================================== diffing TYR.remap.crd.save with TYR.remap.crd PASSED ============================================================== CPPTRAJ: Longer symmetry-corrected RMSD test. diffing afv.rmsd.dat.save with afv.rmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Multidihedral CPPTRAJ: Multidihedral test diffing dihedral.dat with multidih.dat PASSED ============================================================== diffing dihedral2.dat with custom.dat PASSED ============================================================== diffing all.dat.save with all.dat PASSED ============================================================== CPPTRAJ: Multidihedral Nucleotide CHI test diffing chin.dat.save with chin.dat PASSED ============================================================== CPPTRAJ: Multidihedral protein dihedrals test diffing arg.dat.save with arg.dat PASSED ============================================================== CPPTRAJ: Multidihedral cyclic molecule test diffing cyclic.dat.save with cyclic.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Ensemble_MREMD CPPTRAJ: M-REMD sort test. diffing Strip.sorted.crd.0.save with Strip.sorted.crd.0 PASSED ============================================================== diffing Strip.sorted.crd.1.save with Strip.sorted.crd.1 PASSED ============================================================== diffing Strip.sorted.crd.2.save with Strip.sorted.crd.2 PASSED ============================================================== diffing Strip.sorted.crd.3.save with Strip.sorted.crd.3 PASSED ============================================================== diffing Strip.sorted.crd.4.save with Strip.sorted.crd.4 PASSED ============================================================== diffing Strip.sorted.crd.5.save with Strip.sorted.crd.5 PASSED ============================================================== diffing Strip.sorted.crd.6.save with Strip.sorted.crd.6 PASSED ============================================================== diffing Strip.sorted.crd.7.save with Strip.sorted.crd.7 PASSED ============================================================== CPPTRAJ: M-REMD actions test. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing nhbond.dat.save with nhbond.dat PASSED ============================================================== diffing hbavg.dat.save with hbavg.dat PASSED ============================================================== diffing avg.rst7.2.save with avg.rst7.2 PASSED ============================================================== diffing avg.rst7.5.save with avg.rst7.5 PASSED ============================================================== CPPTRAJ: M-REMD ensemble outtraj test. diffing Outtraj.crd.0.save with Outtraj.crd.0 PASSED ============================================================== diffing Outtraj.crd.1.save with Outtraj.crd.1 PASSED ============================================================== CPPTRAJ: M-REMD no sort, running average test diffing RA.dat.save with RA.dat PASSED ============================================================== CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: M-REMD, meltcurve analysis diffing melt.dat.save with melt.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_MakeStructure CPPTRAJ: Basic makestructure test diffing pp2.rst7.save with pp2.rst7 PASSED ============================================================== diffing dihedrals.dat.save with dihedrals.dat PASSED ============================================================== diffing dihedrals2.dat.save with dihedrals2.dat PASSED ============================================================== diffing dihedrals3.dat.save with dihedrals3.dat PASSED ============================================================== CPPTRAJ: Makestructure test with reference. diffing fromref.pdb.save with fromref.pdb.1 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices diffing fromMatrices.crd.save with fromMatrices.crd PASSED ============================================================== diffing ../Test_RMSD/tz2.norotate.crd.save with inverse.crd PASSED ============================================================== CPPTRAJ: Rotate with defined axis diffing TCS.rotated.mol2.save with TCS.rotated.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Integrate CPPTRAJ: Integration test. diffing curve.dat.save with curve.dat PASSED ============================================================== diffing int.dat.save with int.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_NativeContacts CPPTRAJ: NativeContacts test. diffing nc.hp1.ca.dat.save with nc.hp1.ca.dat PASSED ============================================================== diffing nc1.pdb.save with nc1.pdb PASSED ============================================================== diffing nc.hp2.ca.dat.save with nc.hp2.ca.dat PASSED ============================================================== diffing nc2.contacts.dat.save with nc2.contacts.dat PASSED ============================================================== diffing nc2.res.dat.save with nc2.res.dat PASSED ============================================================== diffing NC2.series.dat.save with NC2.series.dat PASSED ============================================================== diffing nc.all.res.dat.save with nc.all.res.dat PASSED ============================================================== diffing native.resmap.gnu.save with native.resmap.gnu PASSED ============================================================== diffing nonnative.resmap.gnu.save with nonnative.resmap.gnu PASSED ============================================================== CPPTRAJ: NativeContacts test, save non-native contacts, residue time series diffing nc4.dat.save with nc4.dat PASSED ============================================================== diffing nc4.nn.dat.save with nc4.nn.dat PASSED ============================================================== diffing nc4.res.dat.save with nc4.res.dat PASSED ============================================================== diffing nc4.contacts.dat.save with nc4.contacts.dat PASSED ============================================================== diffing nc4.nn.pdb.save with nc4.nn.pdb PASSED ============================================================== diffing NC5.respresent.dat.save with NC5.respresent.dat PASSED ============================================================== diffing NC6.ressum.dat.save with NC6.ressum.dat PASSED ============================================================== CPPTRAJ: NativeContacts test, orthorhombic imaging. diffing nc7.dat.save with nc7.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CheckChiral CPPTRAJ: Check chirality test diffing chiral.dat.save with chiral.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Energy CPPTRAJ: Simple energy tests diffing ene.agr.save with ene.agr PASSED ============================================================== CPPTRAJ: Test kinetic energy calculation diffing short.dat.save with short.dat PASSED ============================================================== CPPTRAJ: Test total energy calculation diffing tz2.dat.save with tz2.dat PASSED ============================================================== CPPTRAJ: Test partial energy calculation diffing strip.dat.save with strip.dat PASSED ============================================================== diffing elec.dat.save with elec.dat PASSED ============================================================== diffing vdw.dat.save with vdw.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LESsplit CPPTRAJ: LES split/average test diffing splittraj.0.save with splittraj.0 PASSED ============================================================== diffing avg.crd.save with avg.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals interval -120, phi psi diffing rotations.mdcrd.save with rotations.mdcrd PASSED ============================================================== CPPTRAJ: PermuteDihedrals, random rotations diffing random.mol2.save with random.mol2.1 PASSED ============================================================== diffing random.mol2.save with RAND.mol2 PASSED ============================================================== diffing rand2.mol2.save with rand2.mol2.1 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. diffing fav8.dx.save with fav8.dx PASSED ============================================================== diffing fav8.guv.O.1.ccp4 with fav8.ccp4 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test diffing dihcovar.dat.save with dihcovar.dat PASSED ============================================================== diffing modes.dihcovar.dat.save with modes.dihcovar.dat PASSED ============================================================== diffing dih.project.dat.save with dih.project.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CurveFit CPPTRAJ: Curve fitting test. diffing curve.dat.save with curve.dat PASSED ============================================================== CPPTRAJ: Curve fitting multi-exponential tests. diffing curve.dat.save with curve1.dat PASSED ============================================================== diffing results1.dat.save with results1.dat PASSED ============================================================== diffing Kcurve.dat.save with Kcurve.dat PASSED ============================================================== diffing PKcurve.dat.save with PKcurve.dat PASSED ============================================================== CPPTRAJ: Curve fitting, custom output range. diffing curve2.dat.save with curve2.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Multicurve CPPTRAJ: Multicurve test diffing curves.agr.save with curves.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_DataSetAverage CPPTRAJ: Data set averaging and averaging over all sets test. diffing output.dat.save with output.dat PASSED ============================================================== diffing avg.dat.save with avg.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test diffing dotproduct.dat.save with dotproduct.dat PASSED ============================================================== diffing v1init_dot_v1.dat.save with v1init_dot_v1.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Esander SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Esander_Short CPPTRAJ: Energy via sander API short tests (GB/PME) diffing gb.dat.save with gb.dat PASSED ============================================================== diffing pme.dat.save with pme.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Temperature CPPTRAJ: Temperature test. diffing T.dat.save with T.dat PASSED ============================================================== CPPTRAJ: Temperature with SHAKE on hydrogens. diffing T2.dat.save with T2.dat PASSED ============================================================== CPPTRAJ: Temperature with SHAKE on all atoms. diffing T3.dat.save with T3.dat PASSED ============================================================== diffing T3.dat.save with T4.dat PASSED ============================================================== CPPTRAJ: Temperature calc with extra points. diffing T.XP.agr.save with T.XP.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Spline CPPTRAJ: Spline test diffing spline.dat.save with spline.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_KDE CPPTRAJ: KDE test. diffing kde.dat.save with kde.dat PASSED ============================================================== CPPTRAJ: KDE with Kullback-Leibler divergence test diffing kl.dat.save with kl.dat PASSED ============================================================== diffing final.dat.save with final.dat PASSED ============================================================== diffing divergence.dat.save with divergence.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Wavelet CPPTRAJ: Wavelet analysis test diffing wavelet.gnu.save with wavelet.gnu PASSED ============================================================== CPPTRAJ: Wavelet WAFEX test diffing cluster.gnu.save with cluster.gnu PASSED ============================================================== diffing cluster.dat.save with cluster.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CIF CPPTRAJ: CIF read test diffing 1LE1.pdb.save with 1LE1.pdb PASSED ============================================================== CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Generate offset traj from CIF diffing temp1.crd with temp2.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_PDB CPPTRAJ: PDB format read/write test diffing test.pdb.save with test.pdb PASSED ============================================================== diffing chainA.dat.save with chainA.dat PASSED ============================================================== diffing oresnum.dat.save with oresnum.dat PASSED ============================================================== CPPTRAJ: PQR file write with various radii diffing tz2.pqr.gb.pdb.save with tz2.pqr.gb.pdb PASSED ============================================================== diffing tz2.pqr.parse.pdb.save with tz2.pqr.parse.pdb PASSED ============================================================== diffing tz2.pqr.vdw.pdb.save with tz2.pqr.vdw.pdb PASSED ============================================================== diffing tz2.plain.pdb.save with tz2.plain.pdb PASSED ============================================================== diffing tz2.het.pdb.save with tz2.het.pdb PASSED ============================================================== CPPTRAJ: PDB filter alternate atom location IDs test diffing altloca.pdb.save with altloca.pdb PASSED ============================================================== CPPTRAJ: Adding PDB info to topology diffing 2b5t.fromparm.pdb.save with 2b5t.fromparm.pdb PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Align CPPTRAJ: Align Tests. diffing ../Test_RMSD/rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing ../Test_RMSD/rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== diffing ../Test_RMSD/rmsd.reftraj.dat.save with rmsd.reftraj.dat PASSED ============================================================== CPPTRAJ: Align, unit cell rotation/imaging test. diffing report.0.dat with report.1.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test diffing VAC.agr.save with VAC.agr PASSED ============================================================== diffing diff.dat.save with diff.dat PASSED ============================================================== diffing VAC2.dat.save with VAC2.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_VelFrc CPPTRAJ: Test combining coordinates, velocities, and forces. CPPTRAJ: Test using velocities as coordinates. diffing Vel.crd.save with Vel.crd PASSED ============================================================== CPPTRAJ: Test writing velocities (MDVEL) diffing Vel.crd.save with Vel1.crd PASSED ============================================================== CPPTRAJ: Test using forces as coordinates. diffing Frc.crd.save with Frc.crd PASSED ============================================================== CPPTRAJ: Test writing forces (MDFRC) diffing Frc.crd.save with Frc1.crd PASSED ============================================================== CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. diffing CrdFrcVel.nc with fromncrst.nc PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_RotateDihedral CPPTRAJ: Rotate dihedral to target value. diffing tz2.rotate.1.mol2.save with tz2.rotate.1.mol2 PASSED ============================================================== CPPTRAJ: Rotate dihedral by increment diffing tz2.rotate.1.mol2.save with tz2.rotate.2.mol2 PASSED ============================================================== CPPTRAJ: Rotate dihedral in TRAJ data set diffing tz2.rotate.1.mol2.save with tz2.rotate.3.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_DataSetCmd CPPTRAJ: Data Set commands test diffing avg.dat.save with avg.dat PASSED ============================================================== diffing D4.dat.save with D4.dat PASSED ============================================================== diffing matrix.dat.save with matrix.dat PASSED ============================================================== diffing matrix.dat.save with matrix2.dat PASSED ============================================================== diffing Keep1.dat.save with Keep1.dat PASSED ============================================================== diffing Keep2.dat.save with Keep2.dat PASSED ============================================================== diffing Keep1.dat.save with Drop1.dat PASSED ============================================================== diffing Keep2.dat.save with Drop2.dat PASSED ============================================================== diffing VXYZ.dat.save with VXYZ.dat PASSED ============================================================== diffing Invert.dat.save with Invert.dat PASSED ============================================================== diffing Drop3.dat.save with Drop3.dat PASSED ============================================================== diffing Keep3.dat.save with Keep3.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Remap CPPTRAJ: Remap Test diffing ../Test_AtomMap/reordered.mol2.save with reordered.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CompareTop CPPTRAJ: Compare topology test diffing parm.diff.save with parm.diff PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Filter CPPTRAJ: Basic filter test diffing ../Test_Outtraj/maxmin.crd.save with filter.crd PASSED ============================================================== diffing filter.dat.save with filter.dat PASSED ============================================================== CPPTRAJ: Data filter test. diffing datafilter.dat.save with datafilter.dat PASSED ============================================================== diffing A2.filtered.dat.save with A2.filtered.dat PASSED ============================================================== CPPTRAJ: Filter matrix test. diffing count.dat.save with count.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CombineCrd CPPTRAJ: Combine COORDS test. diffing Final.PRY.mol2.save with Final.PRY.mol2 PASSED ============================================================== CPPTRAJ: Combine COORDS test with box info. diffing combinedParm.parm7.save with combinedParm.parm7 PASSED ============================================================== diffing combinedCrd.crd.save with combinedCrd.crd PASSED ============================================================== CPPTRAJ: Split coords and recombine test. diffing E1.dat with E2.dat PASSED ============================================================== diffing ../FtuFabI.NAD.TCL.parm7 with FabI.NDP.TCS.parm7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_TopInfo CPPTRAJ: Topology info print test. diffing atoms.dat.save with atoms.dat PASSED ============================================================== diffing residues.dat.save with residues.dat PASSED ============================================================== diffing bonds.dat.save with bonds.dat PASSED ============================================================== diffing angles.dat.save with angles.dat PASSED ============================================================== diffing dihedrals.dat.save with dihedrals.dat PASSED ============================================================== diffing masscharge.dat.save with masscharge.dat PASSED ============================================================== diffing molecules.dat.save with molecules.dat PASSED ============================================================== diffing molshort.dat.save with molshort.dat PASSED ============================================================== diffing molselect.dat.save with molselect.dat PASSED ============================================================== diffing molselect2.dat.save with molselect2.dat PASSED ============================================================== diffing ChargeMass.dat.save with ChargeMass.dat PASSED ============================================================== CPPTRAJ: Topology info with reference coords test diffing values.dat.save with values.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test diffing cpptraj.nc.save with cpptraj.nc PASSED ============================================================== CPPTRAJ: TRR force/velocity read -> TRR write test diffing nvt.2frame.trr with cpptraj.trr PASSED ============================================================== CPPTRAJ: CRD => TRR CPPTRAJ: TRR => CRD diffing ../tz2.truncoct.crd with temp.crd PASSED ============================================================== CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: TRR (appended) => CRD diffing ../tz2.truncoct.crd with temp.crd PASSED ============================================================== CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: TRR with offset diffing total1.out with total2.out PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_GromacsXtc CPPTRAJ: XTC read test diffing cpptraj.nc.save with cpptraj.nc PASSED ============================================================== CPPTRAJ: CRD => XTC CPPTRAJ: XTC => CRD diffing temp.crd.save with temp.crd PASSED ============================================================== CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: XTC (appended) => CRD diffing temp.crd.save with temp.crd PASSED ============================================================== CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: XTC with offset diffing total1.out with total2.out PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_GromacsTNG CPPTRAJ: TNG read test diffing temperature.dat.save with temperature.dat PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing ene.dat.save with ene.dat PASSED ============================================================== CPPTRAJ: TNG read test (with offset) diffing offset.temperature.dat.save with offset.temperature.dat PASSED ============================================================== diffing offset.rmsd.dat.save with offset.rmsd.dat PASSED ============================================================== diffing offset.ene.dat.save with offset.ene.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Ewald CPPTRAJ: Direct sum test diffing directsum.0.save with directsum.0 PASSED ============================================================== CPPTRAJ: Ewald test (NaCl crystal) diffing ewald.dat.save with ewald.dat PASSED ============================================================== CPPTRAJ: Ewald test (trunc. oct) diffing ew_tz2.dat.save with ew_tz2.dat PASSED ============================================================== CPPTRAJ: Ewald test (partial system, trunc. oct) diffing ew_partial.dat.save with ew_partial.dat PASSED ============================================================== Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (trunc. oct), 10 frames Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (ortho), 10 frames ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) diffing nacl.dat.save with nacl.dat PASSED ============================================================== CPPTRAJ: Particle mesh Ewald test (trunc. oct) diffing tz2n.dat.save with tz2n.dat PASSED ============================================================== CPPTRAJ: Particle mesh Ewald test (ortho) diffing tz2o.dat.save with tz2o.dat PASSED ============================================================== CPPTRAJ: Particle mesh Ewald test (ortho, with mask) diffing mtz2o.dat.save with mtz2o.dat PASSED ============================================================== CPPTRAJ: PME test (partial system, trunc. oct) diffing pme_partial.dat.save with pme_partial.dat PASSED ============================================================== PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: PME test (trunc. oct), 10 frames ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LJ_PME CPPTRAJ: LJ PME test. diffing ene.dat.save with ene.dat PASSED ============================================================== CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: LJ PME kappa sweep test, 0.35 diffing ene.dat.0 with ene.dat.1 PASSED ============================================================== CPPTRAJ: LJ PME kappa sweep test, 0.45 diffing ene.dat.0 with ene.dat.2 PASSED ============================================================== CPPTRAJ: LJ PME kappa sweep test, 0.5 diffing ene.dat.0 with ene.dat.3 PASSED ============================================================== CPPTRAJ: LJ with switch function test diffing switch.dat.save with switch.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_TI CPPTRAJ: TI analysis test. diffing skip.agr.save with skip.agr PASSED ============================================================== diffing curve.agr.save with curve.agr PASSED ============================================================== diffing avg.dat.save with avg.dat PASSED ============================================================== diffing bs.dat.save with bs.dat PASSED ============================================================== diffing incr.crv.agr.save with incr.crv.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_FixImagedBonds CPPTRAJ: Fix imaged bonds test (Ortho.) diffing fixed.rst7.save with fixed.rst7 PASSED ============================================================== CPPTRAJ: Fix imaged bonds test (Non-ortho.) diffing unimage.crd.save with unimage.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Distance CPPTRAJ: Distance tests diffing dist.dat.save with dist.dat PASSED ============================================================== CPPTRAJ: Orthogonal imaged distance diffing ortho.dat.save with ortho.dat PASSED ============================================================== CPPTRAJ: Non-orthogonal imaged distance diffing truncoct.dat.save with truncoct.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Volume CPPTRAJ: Volume tests diffing vol.dat.save with vol.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_SetVelocity CPPTRAJ: Set Velocity test diffing tz2.vel.rst7.save with tz2.vel.rst7 PASSED ============================================================== diffing V1.dat.save with V1.dat PASSED ============================================================== CPPTRAJ: Scale velocity test diffing tz2.scale.rst7.save with tz2.scale.rst7 PASSED ============================================================== CPPTRAJ: Add velocity test diffing tz2.add.rst7.save with tz2.add.rst7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Remlog CPPTRAJ: Replica log read/analyze test. diffing trepidx.agr.save with trepidx.agr PASSED ============================================================== diffing accept.dat.save with accept.dat PASSED ============================================================== diffing mremdreptime.dat.save with mremdreptime.dat PASSED ============================================================== diffing ph.repidx.agr.save with ph.repidx.agr PASSED ============================================================== diffing ph.stats.dat.save with ph.stats.dat PASSED ============================================================== diffing tcharmm.accept.dat.save with tcharmm.accept.dat PASSED ============================================================== diffing tcharmm.edata.dat.save with tcharmm.edata.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_AreaPerMol CPPTRAJ: Area per molecule test diffing apm.dat.save with apm.dat PASSED ============================================================== diffing apm.dat.save with areaxy.dat PASSED ============================================================== diffing apm.dat.save with mask.dat PASSED ============================================================== diffing apm.dat.save with mask2.dat PASSED ============================================================== diffing areaxz.dat with xz.dat PASSED ============================================================== diffing areayz.dat with yz.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) diffing First.pdb.1.save with First.pdb.1 PASSED ============================================================== diffing Second.pdb.1.save with Second.pdb.1 PASSED ============================================================== diffing Third.pdb.1.save with Third.pdb.1 PASSED ============================================================== diffing Fourth.pdb.1.save with Fourth.pdb.1 PASSED ============================================================== CPPTRAJ: Distance-based atom mask tests (molecule) diffing Fifth.pdb.1.save with Fifth.pdb.1 PASSED ============================================================== diffing Sixth.pdb.1.save with Sixth.pdb.1 PASSED ============================================================== CPPTRAJ: Distance-based atom mask tests (residue center) diffing Seventh.pdb.1.save with Seventh.pdb.1 PASSED ============================================================== diffing Eighth.pdb.1.save with Eighth.pdb.1 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Calc CPPTRAJ: Calc test diffing calc.dat.save with calc.dat PASSED ============================================================== CPPTRAJ: Calc test with data sets diffing mag.dat.save with mag.dat PASSED ============================================================== diffing mag2.dat.save with mag2.dat PASSED ============================================================== CPPTRAJ: Test math functions diffing sumtotal.dat.save with sumtotal.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CalcState CPPTRAJ: Calcstate test diffing state.dat.save with state.dat PASSED ============================================================== diffing curve.dat.save with curve.dat PASSED ============================================================== diffing states.dat.save with states.dat PASSED ============================================================== diffing trans.dat.save with trans.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Change CPPTRAJ: Change atom and residue name tests diffing ala3.mod.pdb.save with ala3.mod.pdb PASSED ============================================================== CPPTRAJ: Change chain ID test diffing ala3.chain.pdb.save with ala3.chain.pdb PASSED ============================================================== CPPTRAJ: Change chain ID of COORDS set test diffing ala3.chain.pdb.save with crdala3.chain.pdb PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CreateReservoir CPPTRAJ: Create RREMD NetCDF reservoir test diffing testres.bins.nc.save with testres.bins.nc PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_FixAtomOrder CPPTRAJ: Out of order molecules test diffing reorder.outoforder.parm7.save with reorder.outoforder.parm7 PASSED ============================================================== diffing reorder.mdcrd.save with reorder.mdcrd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LowestCurve CPPTRAJ: LowestCurve test diffing All.agr.save with All.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_MinImage CPPTRAJ: Minimum Image test. diffing min.dat.save with min.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Regress CPPTRAJ: Linear regression test. diffing statsout.dat.save with statsout.dat PASSED ============================================================== diffing regress.dat.save with regress.dat PASSED ============================================================== diffing Y.dat.save with Y.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Rst CPPTRAJ: Generate restraints (rst) test diffing output.save with output PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Pairwise CPPTRAJ: Pairwise tests diffing pair.dat.save with pair.dat PASSED ============================================================== diffing energy.dat.save with energy.dat PASSED ============================================================== diffing avg.dat.save with avg.dat PASSED ============================================================== diffing map.vdw.gnu.save with map.vdw.gnu PASSED ============================================================== diffing map.elec.gnu.save with map.elec.gnu PASSED ============================================================== diffing ref.cut.mol2.eelec.mol2.1.save with ref.cut.mol2.eelec.mol2.1 PASSED ============================================================== diffing ref.cut.mol2.evdw.mol2.1.save with ref.cut.mol2.evdw.mol2.1 PASSED ============================================================== diffing ref.ene.pdb.save with ref.ene.pdb PASSED ============================================================== CPPTRAJ: Pairwise test, partial system diffing ndptcs.dat.save with ndptcs.dat PASSED ============================================================== diffing ndptcs.ene.dat.save with ndptcs.ene.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_ParmBox CPPTRAJ: Parmbox test diffing out.parm7.save with out.parm7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Solvent CPPTRAJ: Test solvent command with closest diffing closest10.mol2.save with closest10.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Translate CPPTRAJ: Translate coordinates by delta test diffing translate.2.11.mol2.save with translate.2.11.mol2 PASSED ============================================================== CPPTRAJ: Translate to specific coordinates test diffing trp.topoint.1.2.3.mol2.save with trp.topoint.1.2.3.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_ReplicateCell CPPTRAJ: Replicate cell test diffing cell.mol2.save with cell.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test diffing scale.res1.0.5.dat.save with scale.res1.0.5.dat PASSED ============================================================== CPPTRAJ: Scale dihedral force constant with 'useall' diffing scale.N.C.CA.0.5.dat.save with scale.N.C.CA.0.5.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_PhiPsi CPPTRAJ: Phipsi test diffing phipsi.dat.save with phipsi.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Control CPPTRAJ: Loop tests diffing TRP.vec.dat.save with TRP.vec.dat PASSED ============================================================== diffing TRP.rms.dat.save with TRP.rms.dat PASSED ============================================================== diffing TRP.CA.dist.dat.save with TRP.CA.dist.dat PASSED ============================================================== diffing TRP.tocenter.dat.save with TRP.tocenter.dat PASSED ============================================================== diffing nh.dat.save with nh.dat PASSED ============================================================== diffing rms.nofit.dat.save with rms.nofit.dat PASSED ============================================================== diffing last10.dat.save with last10.dat PASSED ============================================================== CPPTRAJ: Test set command diffing testset.dist.dat.save with testset.dist.dat PASSED ============================================================== CPPTRAJ: Test reading comma-separated list of strings diffing distance.dat.save with distance.dat PASSED ============================================================== CPPTRAJ: Test nested loops and variables in loops diffing nested.agr.save with nested.agr PASSED ============================================================== CPPTRAJ: Test loop over data set blocks diffing EndToEnd1.dat.save with EndToEnd1.dat PASSED ============================================================== diffing EndToEnd2.agr.save with EndToEnd2.agr PASSED ============================================================== CPPTRAJ: Test for filename wildcards and oversets diffing DataOut.dat.save with DataOut.dat PASSED ============================================================== CPPTRAJ: Test nested mask loops diffing nested2.dat.save with nested2.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_InfraredSpec CPPTRAJ: Infrared spectrum calculation test diffing irspec.dat.save with irspec.dat PASSED ============================================================== diffing raw.dat.save with raw.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Cphstats CPPTRAJ: Explicit pH REMD ensemble data read / sort diffing sorted.pH_1.00.save with sorted.pH_1.00 PASSED ============================================================== diffing sorted.pH_2.00.save with sorted.pH_2.00 PASSED ============================================================== diffing sorted.pH_3.00.save with sorted.pH_3.00 PASSED ============================================================== diffing sorted.pH_4.00.save with sorted.pH_4.00 PASSED ============================================================== diffing sorted.pH_5.00.save with sorted.pH_5.00 PASSED ============================================================== diffing sorted.pH_6.00.save with sorted.pH_6.00 PASSED ============================================================== CPPTRAJ: Constant pH stats test diffing stats.dat.save with stats.dat PASSED ============================================================== diffing frac.agr.save with frac.agr PASSED ============================================================== CPPTRAJ: Sorted implicit constant pH stats test diffing implicit.sorted.dat.save with implicit.sorted.dat PASSED ============================================================== CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats diffing smallimplicit.sorted.0.cpout.save with smallimplicit.sorted.0.cpout PASSED ============================================================== diffing smallimplicit.sorted.1.cpout.save with smallimplicit.sorted.1.cpout PASSED ============================================================== diffing smallimplicit.sorted.2.cpout.save with smallimplicit.sorted.2.cpout PASSED ============================================================== diffing smallimplicit.sorted.3.cpout.save with smallimplicit.sorted.3.cpout PASSED ============================================================== diffing smallimplicit.stats.dat.save with smallimplicit.stats.dat PASSED ============================================================== CPPTRAJ: Unsorted pH read/write test diffing ExplicitRemd/cpout.004 with explicit.004.cpout PASSED ============================================================== diffing SmallImplicitRemd/run0.cpout.001 with implicit.001.cpout PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 CPPTRAJ: Command line test trajectory args test, part 2 diffing test1.crd.save with test1.crd PASSED ============================================================== CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Command line wildcard test, part 2 diffing res.save with res PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_XYZformat CPPTRAJ: XYZ format write CPPTRAJ: Atom XYZ format read, test 1 diffing test1.crd.save with test1.crd PASSED ============================================================== CPPTRAJ: Atom XYZ format read, test 2 diffing test1.crd.save with test2.crd PASSED ============================================================== CPPTRAJ: Atom XYZ format read, test 3 diffing test1.crd.save with test3.crd PASSED ============================================================== CPPTRAJ: Atom XYZ format read, test 4 diffing test1.crd.save with test4.crd PASSED ============================================================== CPPTRAJ: Atom XYZ format read, test 5 diffing test1.crd.save with test5.crd PASSED ============================================================== CPPTRAJ: Atom XYZ format read, test 6 diffing test1.crd.save with test6.crd PASSED ============================================================== CPPTRAJ: Read regular XYZ format with box info in comments. diffing traj.crd.save with traj.crd PASSED ============================================================== CPPTRAJ: Write regular XYZ format with box info in comments. diffing traj.xyz with cpptraj.traj.xyz PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Hausdorff CPPTRAJ: Simple Hausdorff distance test. diffing hd.dat.save with hd.dat PASSED ============================================================== CPPTRAJ: Hausdorff distance of 2D rms output test. diffing hausdorff.matrix.gnu.save with hausdorff.matrix.gnu PASSED ============================================================== CPPTRAJ: Hausdorff distance of 2D rms output test. diffing hausdorff.matrix.gnu.save with hausdorff.fullmatrix.gnu PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_CatCrd CPPTRAJ: Concatenate COORDS data set test diffing cat.crd.save with cat.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_XtalSymm CPPTRAJ: XtalSymm Reference diffing mdAsuOnly.pdb.save with mdAsuOnly.pdb PASSED ============================================================== CPPTRAJ: XtalSymm Reimaging by Atom diffing mdSolventByAtom.pdb.save with mdSolventByAtom.pdb PASSED ============================================================== CPPTRAJ: XtalSymm Reimaging by Molecule diffing mdSolventByMolecule.pdb.save with mdSolventByMolecule.pdb PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Time CPPTRAJ: Add time to restart test diffing withtime.rst7.save with withtime.rst7 PASSED ============================================================== CPPTRAJ: Remove time from restart test diffing ../tz2.rst7 with notime.rst7 PASSED ============================================================== CPPTRAJ: Add time to trajectory test diffing withtime.nc.save with withtime.nc PASSED ============================================================== CPPTRAJ: Modify time info test. diffing modtime.rst7.save with modtime.rst7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_SplitCoords CPPTRAJ: SplitCoords test diffing out.crd.save with out.crd PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_DihedralRMS CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) diffing dihrms.dat.save with dihrms.dat PASSED ============================================================== diffing dihrms.dat.save with toref.dat PASSED ============================================================== diffing totraj.dat.save with totraj.dat PASSED ============================================================== CPPTRAJ: Dihedral RMSD test (to previous) diffing previous.dat.save with previous.dat PASSED ============================================================== CPPTRAJ: Dihedral RMS fluctuation test. diffing phipsifluct.dat.save with phipsifluct.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Slope CPPTRAJ: Finite difference test. diffing curve.agr.save with curve.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Diagmatrix CPPTRAJ: MW covariance matrix thermo analysis test diffing MyThermo.dat.save with MyThermo.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Emin CPPTRAJ: Basic energy minimization test. diffing cpptraj.ene.dat.save with cpptraj.ene.dat PASSED ============================================================== CPPTRAJ: Energy minimization with angle term test. diffing cpptraj.angle.dat.save with cpptraj.angle.dat PASSED ============================================================== CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. diffing cpptraj.dihedral.dat.save with cpptraj.dihedral.dat PASSED ============================================================== CPPTRAJ: Energy minimization with nonbond term test. diffing cpptraj.nonbond.dat.save with cpptraj.nonbond.dat PASSED ============================================================== OpenMM basic energy minimization tests requires OpenMM. Cpptraj was compiled without OpenMM support. Skipped test: OpenMM basic energy minimization tests ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_EvalPlateau CPPTRAJ: Evalulate plateau test diffing Eval.results.save with Eval.results PASSED ============================================================== diffing Eval.agr.save with Eval.agr PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Graft CPPTRAJ: Graft test diffing Final.graft.mol2.save with Final.graft.mol2 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Flatten CPPTRAJ: Flatten test. diffing flatten.dat.save with flatten.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Random CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs diffing random.dat.save with random.dat PASSED ============================================================== CPPTRAJ: PCG32 RNG test. diffing pcg32.dat.save with pcg32.dat PASSED ============================================================== CPPTRAJ: Test Stdlib RNG diffing stdlib.dat.save with stdlib.dat PASSED ============================================================== CPPTRAJ: Test Mersenne Twister RNG diffing mt.dat.save with mt.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_MultiPucker CPPTRAJ: MultiPucker command test diffing nucleic.dat.save with nucleic.dat PASSED ============================================================== CPPTRAJ: MultiPucker 5-member ring pucker, Cremer & Pople Furanoid test diffing furanoid.dat.save with furanoid.dat PASSED ============================================================== CPPTRAJ: MultiPucker 6-member ring pucker, Cremer & Pople Pyranoid test diffing pyranoid.type.dat.save with pyranoid.type.dat PASSED ============================================================== diffing pyranoid.auto.dat.save with pyranoid.auto.dat PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_LJC CPPTRAJ: Test reading/writing topology with LJ C coefficients diffing cpptraj.znf_1264.parm7.save with cpptraj.znf_1264.parm7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_HmassRepartition CPPTRAJ: Hydrogen mass repartition test diffing tz2.hmr.parm7.save with tz2.hmr.parm7 PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_PrepareForLeap CPPTRAJ: Prepare PDB 1qos for LEaP diffing leap.1qos.in.save with leap.1qos.in PASSED ============================================================== diffing 1qos.cpptraj.pdb.save with 1qos.cpptraj.pdb PASSED ============================================================== CPPTRAJ: Prepare PDB 4zzw for LEaP diffing leap.4zzw.in.save with leap.4zzw.in PASSED ============================================================== diffing 4zzw.cpptraj.pdb.save with 4zzw.cpptraj.pdb PASSED ============================================================== ******************************************************************************** TEST: /usr/local/amber22/AmberTools/src/cpptraj/test/Test_Keep CPPTRAJ: Keep bridging water test diffing keep.crd.save with keep.crd PASSED ============================================================== CPPTRAJ: Keep bridging water and selected residues test CPPTRAJ: Basic keep test diffing ../Test_Strip/res1.tz2.crd.save with res1.tz2.crd PASSED ============================================================== CPPTRAJ: Keep only 1 bridging water test diffing keep.onlyone.crd.save with keep.onlyone.crd PASSED ============================================================== CPPTRAJ: Keep 2 bridging waters at specified residues test diffing keep.two.crd.save with keep.two.crd PASSED ============================================================== make[5]: Leaving directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make[4]: Leaving directory '/usr/local/amber22/AmberTools/src/cpptraj/test' make[3]: Leaving directory '/usr/local/amber22/AmberTools/src/cpptraj/test' cd pytraj && make make[3]: Entering directory '/usr/local/amber22/AmberTools/test/pytraj' Testing serial pytraj /usr/local/amber22//miniconda/bin/python test.py PASSED ============================= test session starts ============================== platform linux -- Python 3.9.12, pytest-7.1.2, pluggy-1.0.0 -- /usr/local/amber22//miniconda/bin/python cachedir: .pytest_cache rootdir: /usr/local/amber22/AmberTools collecting ... collected 9 items ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_GB PASSED [ 11%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_GB_QMMM PASSED [ 22%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_PME PASSED [ 33%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_PME_QMMM PASSED [ 44%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_PME_with_energy_decompositionr PASSED [ 55%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_frame_indices PASSED [ 66%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_gbneck2nu PASSED [ 77%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_mm_options_as_string PASSED [ 88%] ../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_qm_options_as_string PASSED [100%] ============================== 9 passed in 6.35s =============================== make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/pytraj' cd antechamber && make -k test make[3]: Entering directory '/usr/local/amber22/AmberTools/test/antechamber' cd acdoctor && ./Run.cf diffing antechamber.out.save with antechamber.out PASSED ============================================================== cd bondtype && ./Run.bondtype diffing ABAKOE.prepi.save with ABAKOE.prepi PASSED ============================================================== diffing PFPHHG02.prepi.save with PFPHHG02.prepi PASSED ============================================================== diffing fluorescein2.mol2.save with fluorescein2.mol2 PASSED ============================================================== diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2 PASSED ============================================================== diffing antechamber.out.save with antechamber.out PASSED ============================================================== cd fpph && ./Run.fpph diffing fpph.mol2.save with fpph.mol2 PASSED ============================================================== cd fpph && ./Run.fpph_resp diffing fpph_resp.mol2.save with fpph_resp.mol2 PASSED ============================================================== cd g09 && ./Run.g09 diffing C3H7I.gcrt.save with C3H7I.gcrt PASSED ============================================================== diffing C3H7I.ac.save with C3H7I.ac PASSED ============================================================== diffing C3H7I.prepi.save with C3H7I.prepi PASSED ============================================================== diffing antechamber.out.save with antechamber.out PASSED ============================================================== cd parmchk2 && ./Run.parmchk2 diffing ccl3br.frcmod.save with ccl3br.frcmod PASSED ============================================================== diffing diethylamine.frcmod.save with diethylamine.frcmod PASSED ============================================================== diffing N-methylacetamide.frcmod.save with N-methylacetamide.frcmod PASSED ============================================================== cd residuegen && ./Run.ala diffing ala.ac.save with ala.ac PASSED ============================================================== diffing antechamber.out.save with antechamber.out PASSED ============================================================== diffing ala.esp.save with ala.esp PASSED ============================================================== diffing ala.prep.save with ala.prep PASSED ============================================================== cd sustiva && ./Run.sustiva diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out PASSED ============================================================== diffing prmtop.save with prmtop PASSED ============================================================== cd sustiva && ./Run.sustiva_g2 diffing sustiva_g2.mol2.save with sustiva_g2.mol2 PASSED ============================================================== diffing frcmod_g2.save with frcmod_g2 PASSED ============================================================== diffing leap_g2.out.save with leap_g2.out PASSED ============================================================== diffing prmtop_g2.save with prmtop_g2 PASSED ============================================================== cd tp && ./Run.tp diffing tp.mol2.save with tp.mol2 PASSED ============================================================== diffing antechamber.out.save with antechamber.out PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing frcmod.full.save with frcmod.full PASSED ============================================================== cd multirespfix && ./Run.multirespfix diffing qout_stage2.save with qout_stage2 PASSED ============================================================== Checking for errors in logfile PASSED ============================================================== cd c60 && ./Run.c60 diffing buckyball.mol2.save with buckyball.mol2 PASSED ============================================================== diffing buckyball.gzmat.save with buckyball.gzmat PASSED ============================================================== diffing buckyball.jcrt.save with buckyball.jcrt PASSED ============================================================== diffing buckyball.prepi.save with buckyball.prepi PASSED ============================================================== diffing buckyball.ac.save with buckyball.ac PASSED ============================================================== diffing antechamber.out.save with antechamber.out PASSED ============================================================== cd charge_equlibration && ./Run.equ_charge Step1: run antechamber to generate resp charges with '-eq 0' Step2: run antechamber to generate resp charges with '-eq 1' Step3: run antechamber to generate resp charges with '-eq 2' Step4: run antechamber to generate bcc charges with '-eq 0' Step5: run antechamber to generate bcc charges with '-eq 1' Step6: run antechamber to generate bcc charges with '-eq 2' diffing c4h4cl2_eq0.mol2.save with c4h4cl2_eq0.mol2 PASSED ============================================================== diffing c4h4cl2_eq1.mol2.save with c4h4cl2_eq1.mol2 PASSED ============================================================== diffing c4h4cl2_eq2.mol2.save with c4h4cl2_eq2.mol2 PASSED ============================================================== diffing c5h7cl2_eq0.mol2.save with c5h7cl2_eq0.mol2 PASSED ============================================================== diffing c5h7cl2_eq1.mol2.save with c5h7cl2_eq1.mol2 PASSED ============================================================== diffing c5h7cl2_eq2.mol2.save with c5h7cl2_eq2.mol2 PASSED ============================================================== cd chemokine && ./Run.1b2t diffing 1b2t.mol2.save with 1b2t.mol2 PASSED ============================================================== diffing 1b2t.ac.save with 1b2t.ac PASSED ============================================================== cd tp && ./Run.tp2 diffing tp.mol2.save with tp2.mol2 PASSED ============================================================== diffing frcmod.save with frcmod2 PASSED ============================================================== diffing frcmod2.full.save with frcmod2.full PASSED ============================================================== cd ash && ./Run.ash diffing ash.mol2.save with ash.mol2 PASSED ============================================================== diffing antechamber.out.save with antechamber.out PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd fluorescein && ./Run.fluorescein diffing fluorescein.mol2.save with fluorescein.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd guanine_amber && ./Run.guanine_amber diffing DGN.mol2.save with DGN.mol2 PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/antechamber' cd mdgx/1p7e && ./Test.1p7e diffing energy.dat.save with energy.dat PASSED ============================================================== cd mdgx/NVTwat && ./Test.nvtwat diffing temperature.dat.save with temperature.dat PASSED ============================================================== cd mdgx/MLE && ./Test.mle diffing Eelec.dat.save with Eelec.dat PASSED ============================================================== cd mdgx/Settle && ./Test.settle diffing etot.dat.save with etot.dat PASSED ============================================================== cd mdgx/CMAP && ./Test.cmap diffing energy.dat.save with energy.dat PASSED ============================================================== cd mdgx/MCBarostat && ./Test.mcb diffing vol.dat.save with vol.dat PASSED ============================================================== cd mdgx/TIP4P && ./Test.tip4p diffing temperature.dat.save with temperature.dat PASSED ============================================================== cd mdgx/ForceCalc && ./Test.frcc diffing frceval.dat.save with frceval.dat PASSED ============================================================== cd mdgx/AddEP && ./Test.addep diffing etot.dat.save with etot.dat PASSED ============================================================== cd mdgx/QFit && ./Test.qfit diffing hydrogenQ.dat.save with hydrogenQ.dat PASSED ============================================================== diffing fqpt.dat.save with fqpt.dat PASSED ============================================================== cd mdgx/Triclinic && ./Test.triclinic diffing temperature.dat.save with temperature.dat PASSED ============================================================== cd mdgx/Torsion && ./Test.torsion diffing train.out.save with train.out PASSED ============================================================== diffing someparms.dat.save with someparms.dat PASSED ============================================================== diffing trainpa.out.save with trainpa.out PASSED ============================================================== diffing someparmspa.dat.save with someparmspa.dat PASSED ============================================================== cd mdgx/ConfSamp && ./Test.cs diffing extract.txt.save with extract.txt PASSED ============================================================== diffing conf7.pdb.save with conf7.pdb PASSED ============================================================== diffing conf5.crd.save with conf5.crd PASSED ============================================================== diffing extractr.txt.save with extractr.txt PASSED ============================================================== diffing confr2.crd.save with confr2.crd PASSED ============================================================== cd mdgx/Peptides && ./Test.peptides diffing energy_mts.dat.save with energy_mts.dat PASSED ============================================================== diffing kine_mts.dat.save with kine_mts.dat PASSED ============================================================== diffing bond_mts.dat.save with bond_mts.dat PASSED ============================================================== diffing angl_mts.dat.save with angl_mts.dat PASSED ============================================================== diffing dihe_mts.dat.save with dihe_mts.dat PASSED ============================================================== diffing elec_mts.dat.save with elec_mts.dat PASSED ============================================================== diffing vdw_mts.dat.save with vdw_mts.dat PASSED ============================================================== diffing solv_mts.dat.save with solv_mts.dat PASSED ============================================================== diffing energy_rtt.dat.save with energy_rtt.dat PASSED ============================================================== diffing solv_igb1.dat.save with solv_igb1.dat PASSED ============================================================== diffing solv_igb2.dat.save with solv_igb2.dat PASSED ============================================================== diffing solv_igb5.dat.save with solv_igb5.dat PASSED ============================================================== diffing solv_igb6.dat.save with solv_igb6.dat PASSED ============================================================== diffing solv_igb7.dat.save with solv_igb7.dat PASSED ============================================================== cd mdgx/Topology && ./Test.prmtop diffing nTHR.top.save with nTHR.top PASSED ============================================================== diffing nTHR.crd.save with nTHR.crd PASSED ============================================================== cd mdgx/Topology && ./Test.prmtop_vs diffing nOneBrBnzn.top.save with nOneBrBnzn.top PASSED ============================================================== diffing nOneBrBnzn.crd.save with nOneBrBnzn.crd PASSED ============================================================== cd mdgx/Topology && ./Test.tip4p diffing TIP4P_Flex3.top.save with TIP4P_Flex3.top PASSED ============================================================== diffing TIP4P_Flex3.crd.save with TIP4P_Flex3.crd PASSED ============================================================== diffing TIP4P_FD3.top.save with TIP4P_FD3.top PASSED ============================================================== diffing TIP4P_FD3.crd.save with TIP4P_FD3.crd PASSED ============================================================== diffing TIP4P_FAD3.top.save with TIP4P_FAD3.top PASSED ============================================================== diffing TIP4P_FAD3.crd.save with TIP4P_FAD3.crd PASSED ============================================================== cd mdgx/Topology && ./Test.tip5p diffing TIP5P_Out3.top.save with TIP5P_Out3.top PASSED ============================================================== diffing TIP5P_Out3.crd.save with TIP5P_Out3.crd PASSED ============================================================== cd mdgx/Topology && ./Test.methanol diffing Meoh_FD4.top.save with Meoh_FD4.top PASSED ============================================================== diffing Meoh_FD4.crd.save with Meoh_FD4.crd PASSED ============================================================== cd leap && make -k test make[3]: Entering directory '/usr/local/amber22/AmberTools/test/leap' make test.leap test.params make[4]: Entering directory '/usr/local/amber22/AmberTools/test/leap' AMBERHOME is set to /usr/local/amber22// building force field libraries: '94 ff.. diffing /usr/local/amber22///dat/leap/lib/all_amino94.lib with all_amino94.lib PASSED ============================================================== diffing /usr/local/amber22///dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib PASSED ============================================================== diffing /usr/local/amber22///dat/leap/lib/all_aminont94.lib with all_aminont94.lib PASSED ============================================================== diffing /usr/local/amber22///dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib PASSED ============================================================== diffing /usr/local/amber22///dat/leap/lib/ions94.lib with ions94.lib PASSED ============================================================== loadpdb and saveamberparm: 94 ff.. - aminoan94 comparing topology to earlier leap version.. diffing ff94/all_aminoan94.top with all_aminoan94.top PASSED ============================================================== - aminonc94 comparing topology to earlier leap version.. diffing ff94/all_aminonc94.top with all_aminonc94.top PASSED ============================================================== - dna94 comparing topology to earlier leap version.. diffing ff94/all_dna94.top with all_dna94.top PASSED ============================================================== - rna94 comparing topology to earlier leap version.. diffing ff94/all_rna94.top with all_rna94.top PASSED ============================================================== -------------------------------------------------------------- Notes: - If all tests PASSED, you can 'rm *.log *.out *.lib *.top' - For a discussion of energy differences (sander*.dif) see 0README. - It is common to see round-off differences in the portion of these tests -------------------------------------------------------------- Test of several LEaP features diffing sys1.mbondi2.parm7.save with sys1.mbondi2.parm7 PASSED ============================================================== diffing sys2.mbondi2.parm7.save with sys2.mbondi2.parm7 PASSED ============================================================== diffing sys1.mbondi2.rst7.save with sys1.mbondi2.rst7 PASSED ============================================================== diffing sys1_sys2.mbondi.parm7.save with sys1_sys2.mbondi.parm7 PASSED ============================================================== diffing sys1_sys2.mbondi.rst7.save with sys1_sys2.mbondi.rst7 PASSED ============================================================== diffing d_glu.bondi.parm7.save with d_glu.bondi.parm7 PASSED ============================================================== diffing d_glu.bondi.rst7.save with d_glu.bondi.rst7 PASSED ============================================================== diffing alphabet.pdb.save with alphabet.pdb PASSED ============================================================== diffing alphabet2.pdb.save with alphabet2.pdb PASSED ============================================================== diffing alphabet_wet.pdb.save with alphabet_wet.pdb PASSED ============================================================== diffing alphabet2_wet.pdb.save with alphabet2_wet.pdb PASSED ============================================================== Creating a new-style (Amber 7) topology file with mbondi3 diffing alphabet.mbondi3.parm7.save with alphabet.mbondi3.parm7 PASSED ============================================================== AMBERHOME is set to /usr/local/amber22// Test of LEaP PDB reading diffing loadpdb.out.save with loadpdb.out PASSED ============================================================== Creating a new-style (Amber 7) topology file diffing trx.leaplog.save with trx.leaplog PASSED ============================================================== diffing trx.leapout.save with trx.leapout PASSED ============================================================== diffing trx.parm7.save with trx.parm7 PASSED ============================================================== diffing trx.solv.parm7.save with trx.solv.parm7 PASSED ============================================================== diffing gaff_wildcrd.leaplog.save with gaff_wildcrd.leaplog PASSED ============================================================== diffing gaff_wildcrd.leapout.save with gaff_wildcrd.leapout PASSED ============================================================== diffing gaff_wildcrd.parm7.save with gaff_wildcrd.parm7 PASSED ============================================================== Checking that addIons neutralizes pretty well diffing neg_lys_addions.parm7.save with neg_lys_addions.parm7 PASSED ============================================================== ** Testing prmtop and inpcrd built by tleap with GLYCAM_06j. ** diffing Branches.parm7.save with Branches.parm7 PASSED ============================================================== diffing Branches.rst7.save with Branches.rst7 PASSED ============================================================== diffing Chains.parm7.save with Chains.parm7 PASSED ============================================================== diffing Chains.rst7.save with Chains.rst7 PASSED ============================================================== diffing Derivatives.parm7.save with Derivatives.parm7 PASSED ============================================================== diffing Derivatives.rst7.save with Derivatives.rst7 PASSED ============================================================== diffing Solvate_Ion.parm7.save with Solvate_Ion.parm7 PASSED ============================================================== diffing Solvate_Ion.rst7.save with Solvate_Ion.rst7 PASSED ============================================================== ** Testing prmtop and inpcrd built by tleap with GLYCAM_06EPb. ** diffing EP.parm7.save with EP.parm7 PASSED ============================================================== diffing EP.rst7.save with EP.rst7 PASSED ============================================================== diffing Solvate.parm7.save with Solvate.parm7 PASSED ============================================================== diffing Solvate.rst7.save with Solvate.rst7 PASSED ============================================================== ** Testing prmtop and inpcrd built by tleap with GLYCAM_06j_10. ** diffing Glycoprotein.parm7.save with Glycoprotein.parm7 PASSED ============================================================== diffing Glycoprotein.rst7.save with Glycoprotein.rst7 PASSED ============================================================== ** Testing prmtop and inpcrd built by tleap with GLYCAM_06j_12SB. ** diffing Glycoprotein.parm7.save with Glycoprotein.parm7 PASSED ============================================================== diffing Glycoprotein.rst7.save with Glycoprotein.rst7 PASSED ============================================================== Test application of bond augmentation in advanced force fields. diffing r1p7e.prmtop.save with r1p7e.prmtop PASSED ============================================================== AmberTools >= 16 Test OL3 Chi parameters for RNA. diffing rGACC.tip3p.parm7.save with rGACC.tip3p.parm7 PASSED ============================================================== diffing rGACC.nomin.rst7.save with rGACC.nomin.rst7 PASSED ============================================================== diffing tp3.mdout.save with tp3.mdout PASSED ============================================================== diffing rGACC.OL3.parm7.save with rGACC.OL3.parm7 PASSED ============================================================== diffing rGACC.OL3.rst7.save with rGACC.OL3.rst7 PASSED ============================================================== diffing mdout.save with mdout PASSED ============================================================== AmberTools >= 16 Test Yildirim et al Chi parameters for RNA. diffing rGACC.yildirim.tip3p.parm7.save with rGACC.yildirim.tip3p.parm7 PASSED ============================================================== diffing rGACC.nomin.rst7.save with rGACC.nomin.rst7 PASSED ============================================================== diffing tp3.mdout.save with tp3.mdout PASSED ============================================================== diffing rGACC.Yil.parm7.save with rGACC.Yil.parm7 PASSED ============================================================== diffing rGACC.Yil.rst7.save with rGACC.Yil.rst7 PASSED ============================================================== diffing mdout.save with mdout PASSED ============================================================== AmberTools >= 16 Test Yildirim et al Chi parameters for RNA r(GACU). diffing rGACU.parm7.save with rGACU.parm7 PASSED ============================================================== diffing rGACU.rst7.save with rGACU.rst7 PASSED ============================================================== diffing rGACU.out.save with rGACU.out PASSED ============================================================== Test parameters for protein/DNA/RNA system. AmberTools >= 16 diffing bsc1.4py5.parm7.save with bsc1.4py5.parm7 PASSED ============================================================== diffing 4py5.rst7.save with 4py5.rst7 PASSED ============================================================== diffing bsc1.mdout.save with bsc1.mdout PASSED ============================================================== Test BSC0 parameters. AmberTools >= 16 diffing DDD.bsc0.parm7.save with DDD.bsc0.parm7 PASSED ============================================================== diffing DDD.bsc0.rst7.save with DDD.bsc0.rst7 PASSED ============================================================== diffing mdout.save with mdout PASSED ============================================================== Test BSC1 parameters. AmberTools >= 16 diffing DDD.bsc1.parm7.save with DDD.bsc1.parm7 PASSED ============================================================== diffing ../BSC0/DDD.bsc0.rst7.save with DDD.bsc1.rst7 PASSED ============================================================== diffing mdout.save with mdout PASSED ============================================================== Test OL15 parameters. AmberTools >= 16 diffing DDD.OL15.parm7.save with DDD.OL15.parm7 PASSED ============================================================== diffing ../BSC0/DDD.bsc0.rst7.save with DDD.OL15.rst7 PASSED ============================================================== diffing mdout.save with mdout PASSED ============================================================== AmberTools 16 Test GB radii assignments. Radii set: bondi diffing bondi.parm7.save with bondi.parm7 PASSED ============================================================== diffing bondi.out.save with bondi.out PASSED ============================================================== Radii set: amber6 diffing amber6.parm7.save with amber6.parm7 PASSED ============================================================== diffing amber6.out.save with amber6.out PASSED ============================================================== Radii set: mbondi diffing mbondi.parm7.save with mbondi.parm7 PASSED ============================================================== diffing mbondi.out.save with mbondi.out PASSED ============================================================== Radii set: mbondi2 diffing mbondi2.parm7.save with mbondi2.parm7 PASSED ============================================================== diffing mbondi2.out.save with mbondi2.out PASSED ============================================================== Radii set: parse diffing parse.parm7.save with parse.parm7 PASSED ============================================================== diffing parse.out.save with parse.out PASSED ============================================================== Radii set: mbondi3 diffing mbondi3.parm7.save with mbondi3.parm7 PASSED ============================================================== diffing mbondi3.out.save with mbondi3.out PASSED ============================================================== Test Bergonzo & Cheatham phosphate b.b. parameters for RNA. diffing test.04.GACC.parm7.save with test.04.GACC.parm7 PASSED ============================================================== diffing test.04.GACC.rst7.save with test.04.GACC.rst7 PASSED ============================================================== make[4]: Leaving directory '/usr/local/amber22/AmberTools/test/leap' make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/leap' cd xtalutil/UnitCell && make make[3]: Entering directory '/usr/local/amber22/AmberTools/test/xtalutil/UnitCell' ./Run.UnitCell diffing 2igd_uc.pdb.save with 2igd_uc.pdb PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/xtalutil/UnitCell' cd resp && ./Run.ade RESP stage 1: diffing ade_1st.out.save with ade_1st.out PASSED ============================================================== diffing ade_1st.pch.save with ade_1st.pch PASSED ============================================================== diffing ade_1st_calc.esp.save with ade_1st_calc.esp PASSED ============================================================== RESP stage 2: diffing ade_1st.chg.save with ade_1st.chg PASSED ============================================================== diffing ade_2nd.out.save with ade_2nd.out PASSED ============================================================== diffing ade_2nd.pch.save with ade_2nd.pch PASSED ============================================================== diffing ade_2nd.chg.save with ade_2nd.chg PASSED ============================================================== cd py_resp && ./py_resp_test.run ./py_resp_test.run: 5: [[: not found Missing module f90nml py_resp.py test skipped cd reduce && ./Run.reduce diffing 1ubqH.pdb.save with 1ubqH.pdb PASSED ============================================================== diffing messages.save with messages PASSED ============================================================== cd pbsa_dmp && ./test working on ./Run.dmp.sasopt0 diffing mdout.dmp.min_0.save with mdout.dmp.min_0 PASSED ============================================================== working on ./Run.dmp.sasopt1 diffing mdout.dmp.min_1.save with mdout.dmp.min_1 PASSED ============================================================== working on ./Run.dmp.sasopt2 diffing mdout.dmp.min_2.save with mdout.dmp.min_2 PASSED ============================================================== cd pbsa_crgview && ./Run.ion.min diffing at.out.eneopt1.save with at.out PASSED ============================================================== diffing at.out.eneopt2.save with at.out PASSED ============================================================== cd pbsa_bcopt && ./Run.dmp.min bcoption=5 diffing bc5.mdout.dmp.min.save with bc5.mdout.dmp.min PASSED ============================================================== bcoption=6 diffing bc6.mdout.dmp.min.save with bc6.mdout.dmp.min PASSED ============================================================== bcoption=7 diffing bc7.mdout.dmp.min.save with bc7.mdout.dmp.min PASSED ============================================================== bcoption=9 diffing bc9.mdout.dmp.min.save with bc9.mdout.dmp.min PASSED ============================================================== cd pbsa_saopt && ./Run.dmp.min sasopt=0, saopt=-1 diffing sas0.sa-1.mdout.dmp.min.save with sas0.sa-1.mdout.dmp.min PASSED ============================================================== sasopt=0, saopt=-2 diffing sas0.sa-2.mdout.dmp.min.save with sas0.sa-2.mdout.dmp.min PASSED ============================================================== sasopt=1, saopt=-1 diffing sas1.sa-1.mdout.dmp.min.save with sas1.sa-1.mdout.dmp.min PASSED ============================================================== sasopt=1, saopt=-2 diffing sas1.sa-2.mdout.dmp.min.save with sas1.sa-2.mdout.dmp.min PASSED ============================================================== cd pbsa_tri && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== checking dmp force diffing force.save with force.dat PASSED ============================================================== cd pbsa_rot && ./Run.charge.min diffing mdout.charge.min.save with mdout.charge.min PASSED ============================================================== cd pbsa_lpb && ./Run.lsolver.min bcoption=1 solvopt=1 diffing out.save/mdout.min_bc1_solv1.save with mdout.min_bc1_solv1 PASSED ============================================================== bcoption=1 solvopt=2 diffing out.save/mdout.min_bc1_solv2.save with mdout.min_bc1_solv2 PASSED ============================================================== bcoption=1 solvopt=3 diffing out.save/mdout.min_bc1_solv3.save with mdout.min_bc1_solv3 PASSED ============================================================== bcoption=1 solvopt=4 diffing out.save/mdout.min_bc1_solv4.save with mdout.min_bc1_solv4 PASSED ============================================================== bcoption=5 solvopt=1 diffing out.save/mdout.min_bc5_solv1.save with mdout.min_bc5_solv1 PASSED ============================================================== bcoption=5 solvopt=2 diffing out.save/mdout.min_bc5_solv2.save with mdout.min_bc5_solv2 PASSED ============================================================== bcoption=5 solvopt=3 diffing out.save/mdout.min_bc5_solv3.save with mdout.min_bc5_solv3 PASSED ============================================================== bcoption=5 solvopt=4 diffing out.save/mdout.min_bc5_solv4.save with mdout.min_bc5_solv4 PASSED ============================================================== bcoption=10 solvopt=1 diffing out.save/mdout.min_bc10_solv1.save with mdout.min_bc10_solv1 PASSED ============================================================== bcoption=10 solvopt=2 diffing out.save/mdout.min_bc10_solv2.save with mdout.min_bc10_solv2 PASSED ============================================================== bcoption=10 solvopt=3 diffing out.save/mdout.min_bc10_solv3.save with mdout.min_bc10_solv3 PASSED ============================================================== bcoption=10 solvopt=4 diffing out.save/mdout.min_bc10_solv4.save with mdout.min_bc10_solv4 PASSED ============================================================== cd pbsa_ipb2 && ./Run.110D.min diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== cd pbsa_tsr && ./Run.tsrb.min diffing mdout.tsrb.min.save with mdout.tsrb.min PASSED ============================================================== cd pbsa_radi && ./Run.ion.min diffing ./out.save/Na.inp1.out.save with Na.inp1.out PASSED ============================================================== diffing ./out.save/Na.inp2.out.save with Na.inp2.out PASSED ============================================================== diffing ./out.save/nma.inp1.out.save with nma.inp1.out PASSED ============================================================== diffing ./out.save/nma.inp2.out.save with nma.inp2.out PASSED ============================================================== diffing ./out.save/da.inp1.out.save with da.inp1.out PASSED ============================================================== diffing ./out.save/da.inp2.out.save with da.inp2.out PASSED ============================================================== cd pbsa_npb && ./test pbsa.ncg.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nsor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.asor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.dsor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.ntmg.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nticcg.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nticcg.bc6 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== cd pbsa_frc && ./test dbf_0.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_0.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_1.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_1.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_2.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_2.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_3.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_3.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== cd pbsa_delphi && ./test working on ./Run.1az6.min diffing mdout.1az6.min.save with mdout.1az6.min PASSED ============================================================== working on ./Run.1az6.pqr diffing mdout.1az6.pqr.save with mdout.1az6.pqr PASSED ============================================================== cd pbsa_ligand && ./Run.t4bnz.min diffing mdout.lig.min.save with mdout.lig.min PASSED ============================================================== cd pbsa_ipb4 && ./Run.IIM.min diffing mdout.min_bc6.save with mdout.min_bc6 PASSED ============================================================== cd pbsa_ipb5 && ./Run.ion.min diffing save/Cl.out.save with Cl.out PASSED ============================================================== diffing save/MG.out.save with MG.out PASSED ============================================================== cd pbsa_np3m && ./Run.ion.min diffing 420D.out.save with 420D.out PASSED ============================================================== diffing 420D.dat.save with force.dat PASSED ============================================================== diffing 1F81.out.save with 1F81.out PASSED ============================================================== diffing 1F81.dat.save with force.dat PASSED ============================================================== cd pbsa_memb_test && ./Run.memb.test diffing aquaporin_coil.out.save with aquaporin_coil.out PASSED ============================================================== cd pbsa_phiout && ./Run.dmp.min diffing mdout.dmp.phi1.min.save with mdout.dmp.phi1.min PASSED ============================================================== diffing mdout.dmp.phi2.min.save with mdout.dmp.phi2.min PASSED ============================================================== diffing pbsa_phi.dx.save with pbsa_phi.dx PASSED ============================================================== diffing pbsa_phi.phi.save with pbsa_phi.phi PASSED ============================================================== cd gbnsr6 && ./Run.gbnsr6.min diffing undecan_2_one.alpb.out.save with undecan_2_one.alpb.out PASSED ============================================================== diffing undecan_2_one.radii.out.save with undecan_2_one.radii.out PASSED ============================================================== diffing undecan_2_one.chagb.out.save with undecan_2_one.chagb.out PASSED ============================================================== diffing alpb.out.save with alpb.out PASSED ============================================================== cd parmed/normal_prmtop && ./Run.parmed diffing final.prmtop.save with final.prmtop PASSED ============================================================== diffing prmtop.NBFIX.save with prmtop.NBFIX PASSED ============================================================== diffing prmtop.new_chg.save with prmtop.new_chg PASSED ============================================================== diffing trx.frcmod.save with trx.frcmod PASSED ============================================================== diffing trx.off.save with trx.off PASSED ============================================================== diffing prmtop.mbondi3.save with prmtop.mbondi3 PASSED ============================================================== diffing prmtop.scalenb.save with prmtop.scalenb PASSED ============================================================== diffing prmtop.new_mass.save with prmtop.new_mass PASSED ============================================================== diffing prmtop.new_lj.save with prmtop.new_lj PASSED ============================================================== diffing prmtop.add_AtNum.save with prmtop.add_AtNum PASSED ============================================================== cd parmed/chamber_prmtop && ./Run.parmed diffing prmtop.new_type.save with prmtop.new_type PASSED ============================================================== diffing prmtop.NBFIX.save with prmtop.NBFIX PASSED ============================================================== diffing prmtop.new_chg.save with prmtop.new_chg PASSED ============================================================== diffing prmtop.ZEROMASS.save with prmtop.ZEROMASS PASSED ============================================================== diffing final.prmtop.save with final.prmtop PASSED ============================================================== cd parmed/solvated_prmtop && ./Run.parmed diffing ions_solvent.parm7.save with ions_solvent.parm7 PASSED ============================================================== diffing CM_stripped.parm7.save with CM_stripped.parm7 PASSED ============================================================== diffing CM_stripped.rst7.save with CM_stripped.rst7 PASSED ============================================================== diffing receptor.prmtop.save with receptor.prmtop PASSED ============================================================== diffing receptor.rst7.save with receptor.rst7 PASSED ============================================================== diffing receptor_excluded.prmtop.save with receptor_excluded.prmtop PASSED ============================================================== cd parmed/change_parms && ./Run.parmed diffing bonded_ions.parm7.save with bonded_ions.parm7 PASSED ============================================================== diffing bonded_ions_changed.parm7.save with bonded_ions_changed.parm7 PASSED ============================================================== cd parmed/multifiles && ./Run.parmed diffing new_ala3.parm7.save with new_ala3.parm7 PASSED ============================================================== diffing new_gly3.parm7.save with new_gly3.parm7 PASSED ============================================================== diffing new_ala3.parm7.save with new_ala3_2.parm7 PASSED ============================================================== diffing new_gly3.parm7.save with new_gly3_2.parm7 PASSED ============================================================== cd parmed/add12_6_4 && ./Run.parmed diffing znf_1264.prmtop.save with znf_1264.prmtop PASSED ============================================================== diffing znf_1264.inpcrd.save with znf_1264.inpcrd PASSED ============================================================== diffing Mg_ti1_b_1264.parm7.save with Mg_ti1_b_1264.parm7 PASSED ============================================================== diffing before.parm7 with after.parm7 PASSED ============================================================== diffing 1D23_solv_1264.prmtop.save with 1D23_solv_1264.prmtop PASSED ============================================================== diffing 1D23_solv_1264.inpcrd.save with 1D23_solv_1264.inpcrd PASSED ============================================================== cd parmed/ti_merge && ./Run.parmed diffing abs_merged.inpcrd.save with abs_merged.inpcrd PASSED ============================================================== diffing abs_merged.prmtop.save with abs_merged.prmtop PASSED ============================================================== cd parmed/chamber && ./Run.parmed diffing ala_ala_ala.parm7.save with ala_ala_ala.parm7 PASSED ============================================================== diffing ala_ala_ala.rst7.save with ala_ala_ala.rst7 PASSED ============================================================== diffing dhfr_cmap_pbc.parm7.save with dhfr_cmap_pbc.parm7 PASSED ============================================================== diffing dhfr_cmap_pbc.rst7.save with dhfr_cmap_pbc.rst7 PASSED ============================================================== cd elsize && ./Run.elsize diffing elsize_out.trxox.save with elsize_out.trxox PASSED ============================================================== cd ./sqm/c2h2 && ./Run diffing c2h2.pm3.sp.out.save with c2h2.pm3.sp.out PASSED ============================================================== diffing c2h2.pm6.sp.out.save with c2h2.pm6.sp.out PASSED ============================================================== diffing c2h2.pm3.go.out.save with c2h2.pm3.go.out PASSED ============================================================== diffing c2h2.pm6.go.out.save with c2h2.pm6.go.out PASSED ============================================================== cd ./sqm/ch3f && ./Run diffing ch3f.pm3.sp.out.save with ch3f.pm3.sp.out PASSED ============================================================== diffing ch3f.pm6.sp.out.save with ch3f.pm6.sp.out PASSED ============================================================== diffing ch3f.pm3.go.out.save with ch3f.pm3.go.out PASSED ============================================================== diffing ch3f.pm6.go.out.save with ch3f.pm6.go.out PASSED ============================================================== cd ./sqm/nma && ./Run diffing nma.pm3.sp.out.save with nma.pm3.sp.out PASSED ============================================================== diffing nma.pm6.sp.out.save with nma.pm6.sp.out PASSED ============================================================== diffing nma.dftb.sp.out.save with nma.dftb.sp.out PASSED ============================================================== diffing nma.pm3.go.out.save with nma.pm3.go.out PASSED ============================================================== diffing nma.pm6.go.out.save with nma.pm6.go.out PASSED ============================================================== diffing nma.dftb.go.out.save with nma.dftb.go.out PASSED ============================================================== cd ./sqm/znh+ && ./Run diffing znh+.pm3.sp.out.save with znh+.pm3.sp.out PASSED ============================================================== diffing znh+.znb.sp.out.save with znh+.znb.sp.out PASSED ============================================================== diffing znh+.pm3.go.out.save with znh+.pm3.go.out PASSED ============================================================== diffing znh+.znb.go.out.save with znh+.znb.go.out PASSED ============================================================== cd ./sqm/h2s && ./Run diffing h2s.mndod.sp.out.save with h2s.mndod.sp.out PASSED ============================================================== diffing h2s.pm6.sp.out.save with h2s.pm6.sp.out PASSED ============================================================== diffing h2s.dftb.sp.out.save with h2s.dftb.sp.out PASSED ============================================================== diffing h2s.mndod.go.out.save with h2s.mndod.go.out PASSED ============================================================== diffing h2s.dftb.go.out.save with h2s.dftb.go.out PASSED ============================================================== cd ./sqm/dhplus && ./Run diffing meoh_nh3.pm6-dh+.sp.out.save with meoh_nh3.pm6-dh+.sp.out PASSED ============================================================== diffing meoh_nh3.pm6-dh+.go.out.save with meoh_nh3.pm6-dh+.go.out PASSED ============================================================== cd ./sqm/fecp2 && ./Run diffing fecp2.pm6.sp.out.save with fecp2.pm6.sp.out PASSED ============================================================== cd ./sqm/external_charges && ./Run diffing qm_adenine.pm3.sp.out.save with qm_adenine.pm3.sp.out PASSED ============================================================== diffing qm_thymine.pm3.sp.out.save with qm_thymine.pm3.sp.out PASSED ============================================================== diffing qm_adenine.dftb.sp.out.save with qm_adenine.dftb.sp.out PASSED ============================================================== diffing qm_thymine.dftb.sp.out.save with qm_thymine.dftb.sp.out PASSED ============================================================== cd ./sqm/dftb3 && ./Run diffing h2o.sp.out.save with h2o.sp.out PASSED ============================================================== diffing cysdip.sp.out.save with cysdip.sp.out PASSED ============================================================== diffing lignin.sp.out.save with lignin.sp.out PASSED ============================================================== diffing h2o.go.out.save with h2o.go.out PASSED ============================================================== diffing cysdip.go.out.save with cysdip.go.out PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/spc-kh && ./Run.spc; fi diffing spc.xvv.delhv0.save with spc.xvv.delhv0 PASSED ============================================================== diffing spc.xvv.delhv0_dT.save with spc.xvv.delhv0_dT PASSED ============================================================== diffing spc.xvv.xvv.save with spc.xvv.xvv PASSED ============================================================== diffing spc.xvv.xvv_dT.save with spc.xvv.xvv_dT PASSED ============================================================== diffing spc.xvv.other.save with spc.xvv.other PASSED ============================================================== diffing spc.uvv.save with spc.uvv PASSED ============================================================== diffing spc.gvv.save with spc.gvv PASSED ============================================================== diffing spc.cvv.save with spc.cvv PASSED ============================================================== diffing spc.cvv_dT.save with spc.cvv_dT PASSED ============================================================== diffing spc.therm.save with spc.therm PASSED ============================================================== diffing spc.exnvv.save with spc.exnvv PASSED ============================================================== diffing spc.nvv.save with spc.nvv PASSED ============================================================== diffing spc.n00.save with spc.n00 PASSED ============================================================== diffing spc.q00.save with spc.q00 PASSED ============================================================== diffing spc.hvv.save with spc.hvv PASSED ============================================================== diffing spc.hvv_dT.save with spc.hvv_dT PASSED ============================================================== diffing spc.svv.save with spc.svv PASSED ============================================================== diffing spc.bvv.save with spc.bvv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/spc-psen && ./Run.spc-nacl-3; fi diffing spc-nacl-3.xvv.delhv0.save with spc-nacl-3.xvv.delhv0 PASSED ============================================================== diffing spc-nacl-3.xvv.delhv0_dT.save with spc-nacl-3.xvv.delhv0_dT PASSED ============================================================== diffing spc-nacl-3.xvv.xvv.save with spc-nacl-3.xvv.xvv PASSED ============================================================== diffing spc-nacl-3.xvv.xvv_dT.save with spc-nacl-3.xvv.xvv_dT PASSED ============================================================== diffing spc-nacl-3.xvv.other.save with spc-nacl-3.xvv.other PASSED ============================================================== diffing spc-nacl-3.uvv.save with spc-nacl-3.uvv PASSED ============================================================== diffing spc-nacl-3.gvv.save with spc-nacl-3.gvv PASSED ============================================================== diffing spc-nacl-3.gvv_dT.save with spc-nacl-3.gvv_dT PASSED ============================================================== diffing spc-nacl-3.cvv.save with spc-nacl-3.cvv PASSED ============================================================== diffing spc-nacl-3.cvv_dT.save with spc-nacl-3.cvv_dT PASSED ============================================================== diffing spc-nacl-3.therm.save with spc-nacl-3.therm PASSED ============================================================== diffing spc-nacl-3.exnvv.save with spc-nacl-3.exnvv PASSED ============================================================== diffing spc-nacl-3.nvv.save with spc-nacl-3.nvv PASSED ============================================================== diffing spc-nacl-3.n00.save with spc-nacl-3.n00 PASSED ============================================================== diffing spc-nacl-3.q00.save with spc-nacl-3.q00 PASSED ============================================================== diffing spc-nacl-3.hvv.save with spc-nacl-3.hvv PASSED ============================================================== diffing spc-nacl-3.hvv_dT.save with spc-nacl-3.hvv_dT PASSED ============================================================== diffing spc-nacl-3.svv.save with spc-nacl-3.svv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/spc-hnc && ./Run.spc-lj; fi diffing spc-lj.xvv.delhv0.save with spc-lj.xvv.delhv0 PASSED ============================================================== diffing spc-lj.xvv.delhv0_dT.save with spc-lj.xvv.delhv0_dT PASSED ============================================================== diffing spc-lj.xvv.xvv.save with spc-lj.xvv.xvv PASSED ============================================================== diffing spc-lj.xvv.xvv_dT.save with spc-lj.xvv.xvv_dT PASSED ============================================================== diffing spc-lj.xvv.other.save with spc-lj.xvv.other PASSED ============================================================== diffing spc-lj.uvv.save with spc-lj.uvv PASSED ============================================================== diffing spc-lj.gvv.save with spc-lj.gvv PASSED ============================================================== diffing spc-lj.cvv.save with spc-lj.cvv PASSED ============================================================== diffing spc-lj.therm.save with spc-lj.therm PASSED ============================================================== diffing spc-lj.exnvv.save with spc-lj.exnvv PASSED ============================================================== diffing spc-lj.nvv.save with spc-lj.nvv PASSED ============================================================== diffing spc-lj.n00.save with spc-lj.n00 PASSED ============================================================== diffing spc-lj.q00.save with spc-lj.q00 PASSED ============================================================== diffing spc-lj.hvv.save with spc-lj.hvv PASSED ============================================================== diffing spc-lj.svv.save with spc-lj.svv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/tip3p-kh && ./Run.tip3p; fi diffing tip3p.xvv.delhv0.save with tip3p.xvv.delhv0 PASSED ============================================================== diffing tip3p.xvv.delhv0_dT.save with tip3p.xvv.delhv0_dT PASSED ============================================================== diffing tip3p.xvv.xvv.save with tip3p.xvv.xvv PASSED ============================================================== diffing tip3p.xvv.xvv_dT.save with tip3p.xvv.xvv_dT PASSED ============================================================== diffing tip3p.xvv.other.save with tip3p.xvv.other PASSED ============================================================== diffing tip3p.uvv.save with tip3p.uvv PASSED ============================================================== diffing tip3p.gvv.save with tip3p.gvv PASSED ============================================================== diffing tip3p.cvv.save with tip3p.cvv PASSED ============================================================== diffing tip3p.therm.save with tip3p.therm PASSED ============================================================== diffing tip3p.exnvv.save with tip3p.exnvv PASSED ============================================================== diffing tip3p.nvv.save with tip3p.nvv PASSED ============================================================== diffing tip3p.n00.save with tip3p.n00 PASSED ============================================================== diffing tip3p.q00.save with tip3p.q00 PASSED ============================================================== diffing tip3p.hvv.save with tip3p.hvv PASSED ============================================================== diffing tip3p.svv.save with tip3p.svv PASSED ============================================================== cd kmmd/kmmd_sander && ./Run.kmmd running: /usr/local/amber22///bin/sander diffing mdout.save with mdout PASSED ============================================================== cd kmmd/kmmd_sander_gb && ./Run.kmmd diffing mdout.save with mdout PASSED ============================================================== if [ "" = 'yes' ]; then cd rism3d.periodic/4lzta && ./Run.4lzta.kh.pme; fi if [ "" = 'yes' ]; then cd rism3d.periodic/1ahoa && ./Run.1ahoa.kh.pme; fi cd paramfit && make -k test make[3]: Entering directory '/usr/local/amber22/AmberTools/test/paramfit' cd write_qminput_nma; ./run_test.x *** Create Gaussian Input Files (new prmtop) *** diffing saved_output/Job.0.gjf.saved with Job.0.gjf PASSED ============================================================== diffing saved_output/Job.1.gjf.saved with Job.1.gjf PASSED ============================================================== diffing saved_output/Job.2.gjf.saved with Job.2.gjf PASSED ============================================================== diffing saved_output/Job.3.gjf.saved with Job.3.gjf PASSED ============================================================== diffing saved_output/Job.4.gjf.saved with Job.4.gjf PASSED ============================================================== cd simplex_perfect_fit_NMA; ./run_test.x *** NMA Simplex Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== cd ga_perfect_fit_NMA; ./run_test.x *** NMA Genetic Algorithm Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== diffing saved_output/frcmod.saved with frcmod PASSED ============================================================== cd dihedral_least_squares_NMA; ./run_test.x *** NMA Dihedral Linear Algorithm Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== diffing saved_output/frcmod.saved with frcmod PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/paramfit' cd ../src/mm_pbsa/Examples && AMBER_SOURCE=/usr/local/amber22// ./Run.mmpbsa.test CLEANING CALCULATING TEST: 01_GenerateSnapshots CHECKING IN TEST: 01_GenerateSnapshots CALCULATING TEST: 03_MMPBSA_Binding CHECKING IN TEST: 03_MMPBSA_Binding diffing /usr/local/amber22///AmberTools/src/mm_pbsa/Examples/03_MMPBSA_Binding/test_statistics.out.save with /usr/local/amber22///AmberTools/src/mm_pbsa/Examples/03_MMPBSA_Binding/test_statistics.out PASSED ============================================================== CALCULATING TEST: 05_MMPBSA_Decomp_Residue CHECKING IN TEST: 05_MMPBSA_Decomp_Residue diffing /usr/local/amber22///AmberTools/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/test_statistics.out.save with /usr/local/amber22///AmberTools/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/test_statistics.out possible FAILURE: check /usr/local/amber22///AmberTools/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/test_statistics.out.dif ============================================================== cd ../src/FEW/examples/test && AMBER_SOURCE=/usr/local/amber22// ./Run.few.test ######################################################################### PERFORMING FEW TESTS If all of the tests below fail then check the system specific path to the locally installed Perl libraries. For details on test issues and on how to fix them read: /usr/local/amber22/AmberTools/src/FEW/examples/test/few.log CLEANING PERFORMING TEST 01: Step1 of RESP charge calculation CHECKING IN TEST 01: Step1 of RESP charge calculation diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/gauss_setup/L51a/L51a.gcrt with /usr/local/amber22/AmberTools/src/FEW/examples/test/gauss/L51a/L51a.gcrt PASSED ============================================================== PERFORMING TEST 02: Step2 of RESP charge calculation and setup of MD simulations CHECKING IN TEST 02: Step2 of RESP charge calculation and setup of MD simulations diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/gauss_setup/L51a/L51a.gout.xyz with /usr/local/amber22/AmberTools/src/FEW/examples/test/gauss/L51a/L51a.gout.xyz PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_resp.lib with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/L51a/L51a_resp.lib PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a.frcmod with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/L51a/L51a.frcmod PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_com.pdb with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/L51a/L51a_com.pdb PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_rec.pdb with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/L51a/L51a_rec.pdb PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_lig.pdb with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/L51a/L51a_lig.pdb PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/cryst/L51a_solv_com.crd with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_com.crd PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/cryst/L51a_solv_rec.crd with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_rec.crd PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/cryst/L51a_solv_lig.crd with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_lig.crd PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/lig/equi/md_nvt_red_06.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_resp/L51a/lig/equi/md_nvt_red_06.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/rec/equi/md_nvt_red_06.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_resp/rec/equi/md_nvt_red_06.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/lig/prod/md_prod_001.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_resp/L51a/lig/prod/md_prod_001.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/rec/prod/md_prod_001.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_resp/rec/prod/md_prod_001.in PASSED ============================================================== PERFORMING TEST 03: Setup of MMPBSA calculations according to 1-trajectory approach CHECKING IN TEST 03: Setup of MMPBSA calculations according to 1-trajectory approach diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_r_1t/L51a/snapshots/L51a_lig.crd.5 with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_r_1t/L51a/snapshots/L51a_lig.crd.5 PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_r_1t/L51a/topo/L51a_gb0_pb3_lig.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_r_1t/L51a/topo/L51a_gb0_pb3_lig.top PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_r_1t/L51a/s2_4_1/pb3_gb0/mmpbsa.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_r_1t/L51a/s2_4_1/pb3_gb0/mmpbsa.in PASSED ============================================================== PERFORMING TEST 04: Setup of LIE analysis CHECKING IN TEST 04: Setup of LIE analysis diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/topo/lig.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/topo/lig.top PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/topo/tot.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/topo/tot.top PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/topo/wat.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/topo/wat.top PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/s_lig/md_prod_001_nobox.mdcrd with /usr/local/amber22/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/s_lig/md_prod_001_nobox.mdcrd PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/s_tot/md_prod_001_nobox.mdcrd with /usr/local/amber22/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/s_tot/md_prod_001_nobox.mdcrd PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/s_wat/md_prod_001_nobox.mdcrd with /usr/local/amber22/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/s_wat/md_prod_001_nobox.mdcrd PASSED ============================================================== PERFORMING TEST 05: TI step1, Preparation of coordinate and topology files CHECKING IN TEST 05: TI step1, Preparation of coordinate and toplogy files diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/match_list.txt with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/match_list.txt PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/setup/L51a_lig_TIin.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/setup/L51a_lig_TIin.top PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/setup/L51b_lig_TIin.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/setup/L51b_lig_TIin.top PASSED ============================================================== PERFORMING TEST 06: TI step2A, Preparation of files for TI equilibration CHECKING IN TEST 06: TI step2A, Preparation of files for TI equilibration diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/group_equi01_l2 with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/group_equi01_l2 PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/LFa_equi01_v0_l2.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/LFa_equi01_v0_l2.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/group_prod01_l2 with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/group_prod01_l2 PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/LFa_prod01_v0_l2.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/LFa_prod01_v0_l2.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/LFa_lig_TIin.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/LFa_lig_TIin.top PASSED ============================================================== PERFORMING TEST 07: TI step3, Preparation of files for TI production CHECKING IN TEST 07: TI step3, Preparation of files for TI production diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/TI_results/TI_dG.out with /usr/local/amber22/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/TI_results/TI_dG.out PASSED ============================================================== PERFORMING TEST 08: Setup of MD simulations with explicit membrane and AM1 charges CHECKING IN TEST 08: Setup of MD simulations with explicit membrane and AM1 charges diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_am1.lib with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/AMT/AMT_am1.lib PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_com.pdb with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/AMT/AMT_com.pdb PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_rec.pdb with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/AMT/AMT_rec.pdb PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_lig.pdb with /usr/local/amber22/AmberTools/src/FEW/examples/test/leap/AMT/AMT_lig.pdb PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_am1_setup_membrane/AMT/cryst/AMT_solv_com.crd with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_am1/AMT/cryst/AMT_solv_com.crd PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_am1_setup_membrane/AMT/com/equi/md3npt.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_am1/AMT/com/equi/md3npt.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/MD_am1_setup_membrane/AMT/com/prod/md_prod_001.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/MD_am1/AMT/com/prod/md_prod_001.in PASSED ============================================================== PERFORMING TEST 09: Setup of MMPBSA calculations with implicit membrane CHECKING IN TEST 09: Setup of MMPBSA calculations with implicit membrane diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/snapshots/AMT_com.crd.3 with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/snapshots/AMT_com.crd.3 PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/topo/AMT_gb0_pb3_com.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/topo/AMT_gb0_pb3_com.top PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/s1_3_1/pb3_gb0/mmpbsa.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/s1_3_1/pb3_gb0/mmpbsa.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/pqr_snaps/AMT_rec.pqr.3 with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/pqr_snaps/AMT_rec.pqr.3 file ddtmp._usr_local_amber22_AmberTools_src_FEW_examples_test_saved_calc_a_1t_ImplMem_AMT_pqr_snaps_AMT_rec.pqr.3 is short possible FAILURE: (ignored) check /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/pqr_snaps/AMT_rec.pqr.3.dif ============================================================== PERFORMING TEST 10: Setup of protein-protein 1-trajectory based MM-PBSA calculation with implicit membrane CHECKING IN TEST 10: Setup of protein-protein 1-trajectory based MM-PBSA calculation with implicit membrane diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_p_1t/TGR5_dimer_1-8_-46/snapshots/TGR5_dimer_1-8_-46_lig.crd.2 with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_p_1t/TGR5_dimer_1-8_-46/snapshots/TGR5_dimer_1-8_-46_lig.crd.2 PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_p_1t/TGR5_dimer_1-8_-46/topo/TGR5_dimer_1-8_-46_gb0_pb3_com.top with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_p_1t/TGR5_dimer_1-8_-46/topo/TGR5_dimer_1-8_-46_gb0_pb3_com.top PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_p_1t/TGR5_dimer_1-8_-46/s1_2_1/pb3_gb0_dec/mmpbsa.in with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_p_1t/TGR5_dimer_1-8_-46/s1_2_1/pb3_gb0_dec/mmpbsa.in PASSED ============================================================== diffing /usr/local/amber22/AmberTools/src/FEW/examples/test/saved/calc_p_1t/TGR5_dimer_1-8_-46/pqr_snaps/TGR5_dimer_1-8_-46_rec.pqr.2 with /usr/local/amber22/AmberTools/src/FEW/examples/test/calc_p_1t/TGR5_dimer_1-8_-46/pqr_snaps/TGR5_dimer_1-8_-46_rec.pqr.2 PASSED ============================================================== cd cphstats && ./Run.cphstats diffing md2_cpout.pH_2.00.save with md2_cpout.pH_2.00 PASSED ============================================================== diffing md3_cpout.pH_4.50.save with md3_cpout.pH_4.50 PASSED ============================================================== diffing pH_2.00.calcpka.save with pH_2.00.calcpka PASSED ============================================================== diffing pH_2.50.calcpka.save with pH_2.50.calcpka PASSED ============================================================== diffing pH_3.00.calcpka.save with pH_3.00.calcpka PASSED ============================================================== diffing pH_3.50.calcpka.save with pH_3.50.calcpka PASSED ============================================================== diffing pH_4.00.calcpka.save with pH_4.00.calcpka PASSED ============================================================== diffing pH_4.50.calcpka.save with pH_4.50.calcpka PASSED ============================================================== diffing pH_5.00.calcpka.save with pH_5.00.calcpka PASSED ============================================================== diffing pH_5.50.calcpka.save with pH_5.50.calcpka PASSED ============================================================== diffing pH_6.00.calcpka.save with pH_6.00.calcpka PASSED ============================================================== diffing pH_6.50.calcpka.save with pH_6.50.calcpka PASSED ============================================================== diffing pH_7.00.calcpka.save with pH_7.00.calcpka PASSED ============================================================== diffing pH_7.50.calcpka.save with pH_7.50.calcpka PASSED ============================================================== diffing pH_2.00.calcpka.save with pH_2.00.calcpka PASSED ============================================================== diffing cphstats_output.txt.save with cphstats_output.txt PASSED ============================================================== diffing running_avgs.dat.save with running_avgs.dat PASSED ============================================================== diffing running_avg.dat.save with running_avg.dat PASSED ============================================================== diffing running_pKa.dat.save with running_pKa.dat PASSED ============================================================== diffing chunk.dat.save with chunk.dat PASSED ============================================================== diffing chunk_deprot.dat.save with chunk_deprot.dat PASSED ============================================================== diffing chunk_pka.dat.save with chunk_pka.dat PASSED ============================================================== diffing cumulative.dat.save with cumulative.dat PASSED ============================================================== diffing cumulative_deprot.dat.save with cumulative_deprot.dat PASSED ============================================================== diffing cumulative_pka.dat.save with cumulative_pka.dat PASSED ============================================================== diffing pop.dat.save with pop.dat PASSED ============================================================== diffing conditional.dat.save with conditional.dat PASSED ============================================================== diffing conditional_chunks.dat.save with conditional_chunks.dat PASSED ============================================================== diffing cphstats_output.cpe.txt.save with cphstats_output.cpe.txt PASSED ============================================================== cd cestats && ./Run.cestats diffing md2_ceout.E_0.75000.save with md2_ceout.E_0.75000 PASSED ============================================================== diffing md3_ceout.E_0.81000.save with md3_ceout.E_0.81000 PASSED ============================================================== diffing md4_ceout.E_0.84000.save with md4_ceout.E_0.84000 PASSED ============================================================== diffing md5_ceout.E_0.90000.save with md5_ceout.E_0.90000 PASSED ============================================================== diffing E_0.75.calceo.save with E_0.75.calceo PASSED ============================================================== diffing E_0.78.calceo.save with E_0.78.calceo PASSED ============================================================== diffing E_0.81.calceo.save with E_0.81.calceo PASSED ============================================================== diffing E_0.84.calceo.save with E_0.84.calceo PASSED ============================================================== diffing E_0.87.calceo.save with E_0.87.calceo PASSED ============================================================== diffing E_0.90.calceo.save with E_0.90.calceo PASSED ============================================================== diffing E_0.75.calceo.save with E_0.75.calceo PASSED ============================================================== diffing cestats_output.txt.save with cestats_output.txt PASSED ============================================================== diffing running_avgs.dat.save with running_avgs.dat PASSED ============================================================== diffing running_avg.dat.save with running_avg.dat PASSED ============================================================== diffing running_Eo.dat.save with running_Eo.dat PASSED ============================================================== diffing chunk.dat.save with chunk.dat PASSED ============================================================== diffing chunk_oxid.dat.save with chunk_oxid.dat PASSED ============================================================== diffing chunk_eo.dat.save with chunk_eo.dat PASSED ============================================================== diffing cumulative.dat.save with cumulative.dat PASSED ============================================================== diffing cumulative_oxid.dat.save with cumulative_oxid.dat PASSED ============================================================== diffing cumulative_eo.dat.save with cumulative_eo.dat PASSED ============================================================== diffing pop.dat.save with pop.dat PASSED ============================================================== diffing conditional.dat.save with conditional.dat PASSED ============================================================== diffing conditional_chunks.dat.save with conditional_chunks.dat PASSED ============================================================== diffing cestats_output.cpe.txt.save with cestats_output.cpe.txt PASSED ============================================================== cd charmmlipid2amber && ./Run.charmmlipid2amber diffing charmmlipid2amber.out.save with charmmlipid2amber.out PASSED ============================================================== cd cpinutil && ./Run.cpin Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! Warning: The old format of the CPIN file can only be used for simulations with temp0=300.0! You should use the new format for simulations with temperatures other than 300.0 Kelvins CPIN generation complete! CPIN generation complete! CPIN generation complete! diffing cpin1.save with cpin1 PASSED ============================================================== diffing cpin2.save with cpin2 PASSED ============================================================== diffing cpin3.save with cpin3 PASSED ============================================================== diffing cpin3.save with cpin3.1 PASSED ============================================================== diffing cpin4.save with cpin4 PASSED ============================================================== diffing cpin5.save with cpin5 PASSED ============================================================== diffing cpin6.save with cpin6 PASSED ============================================================== diffing cpin7.save with cpin7 PASSED ============================================================== diffing hewl.op.parm7.save with hewl.op.parm7 PASSED ============================================================== diffing cpin8.save with cpin8 PASSED ============================================================== diffing cpin9.save with cpin9 PASSED ============================================================== cd ceinutil && ./Run.cein CEIN generation complete! CEIN generation complete! CEIN generation complete! CEIN generation complete! CEIN generation complete! CEIN generation complete! CEIN generation complete! diffing cein1.save with cein1 PASSED ============================================================== diffing cein2.save with cein2 PASSED ============================================================== diffing cein3.save with cein3 PASSED ============================================================== diffing cein3.save with cein3.1 PASSED ============================================================== diffing cein4.save with cein4 PASSED ============================================================== diffing cein5.save with cein5 PASSED ============================================================== diffing cein6.save with cein6 PASSED ============================================================== cd cpeinutil && ./Run.cpein CPEIN generation complete! CPEIN generation complete! CPEIN generation complete! CPEIN generation complete! CPEIN generation complete! CPEIN generation complete! diffing cpein1.save with cpein1 PASSED ============================================================== diffing cpein2.save with cpein2 PASSED ============================================================== diffing cpein3.save with cpein3 PASSED ============================================================== diffing cpein4.save with cpein4 PASSED ============================================================== diffing cpein5.save with cpein5 PASSED ============================================================== diffing cpein6.save with cpein6 PASSED ============================================================== cd genremdinputs && ./Run.genremdinputs diffing output1.1d.dat.save with output1.1d.dat PASSED ============================================================== diffing output2.1d.dat.save with output2.1d.dat PASSED ============================================================== diffing groupfile.1d.2.save with groupfile.1d.2 PASSED ============================================================== diffing mdin.1d.rep.002.save with mdin.1d.rep.002 PASSED ============================================================== diffing mdin.1d.1.rep.001.save with mdin.1d.1.rep.001 PASSED ============================================================== diffing mdin.1d.2.rep.003.save with mdin.1d.2.rep.003 PASSED ============================================================== diffing remd.dim.phremd.save with remd.dim.phremd PASSED ============================================================== diffing groupfile.1d.us.save with groupfile.1d.us PASSED ============================================================== diffing mdin.1d.us.rep.001.save with mdin.1d.us.rep.001 PASSED ============================================================== diffing distang.rep.003.save with distang.rep.003 PASSED ============================================================== diffing output.2d.dat.save with output.2d.dat PASSED ============================================================== diffing groupfile.2d.save with groupfile.2d PASSED ============================================================== diffing mdin.2d.rep.002.save with mdin.2d.rep.002 PASSED ============================================================== diffing remd.dim.htremd.save with remd.dim.htremd PASSED ============================================================== diffing output.2d2.dat.save with output.2d2.dat PASSED ============================================================== diffing groupfile.2d2.save with groupfile.2d2 PASSED ============================================================== diffing mdin.2d2.rep.002.save with mdin.2d2.rep.002 PASSED ============================================================== diffing remd.dim.hhremd.save with remd.dim.hhremd PASSED ============================================================== diffing output.3d.dat.save with output.3d.dat PASSED ============================================================== diffing groupfile.3d.save with groupfile.3d PASSED ============================================================== diffing mdin.3d.rep.002.save with mdin.3d.rep.002 PASSED ============================================================== diffing remd.dim.ephtremd.save with remd.dim.ephtremd PASSED ============================================================== cd fitpkaeo && ./Run.fitpkaeo diffing output.pka.dat.save with output.pka.dat PASSED ============================================================== diffing output.pka.verbose.dat.save with output.pka.verbose.dat PASSED ============================================================== diffing output.eo.dat.save with output.eo.dat PASSED ============================================================== diffing output.eo.verbose.dat.save with output.eo.verbose.dat PASSED ============================================================== cd fixremdcouts && ./Run.fixremdcouts diffing reord.1d.cpout.E_0.7500000.save with reord.1d.pt1.cpout.E_0.7500000 PASSED ============================================================== diffing reord.1d.cpout.E_0.7500000.save with reord.1d.both.cpout.E_0.7500000 PASSED ============================================================== diffing reord.1d.ceout.E_0.8100000.save with reord.1d.pt2.ceout.E_0.8100000 PASSED ============================================================== diffing reord.1d.ceout.E_0.8100000.save with reord.1d.both.ceout.E_0.8100000 PASSED ============================================================== diffing reord.2d.cpout.E_0.8400000.T_280.00.save with reord.2d.cpout.E_0.8400000.T_280.00 PASSED ============================================================== diffing reord.2d.ceout.E_0.8400000.T_280.00.save with reord.2d.ceout.E_0.8400000.T_280.00 PASSED ============================================================== diffing reord.3d.cpout.E_0.8100000.pH_10.500.T_300.00.save with reord.3d.cpout.E_0.8100000.pH_10.500.T_300.00 PASSED ============================================================== diffing reord.3d.ceout.E_0.8100000.pH_10.500.T_300.00.save with reord.3d.ceout.E_0.8100000.pH_10.500.T_300.00 PASSED ============================================================== cd pymsmt/mcpb/g03-ff14SB && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/g09-ff14SB && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/g09-ff19SB && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/g16-ff14SB && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/g16-ff14SB-zmx && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/g16-ff19SB && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/g16-ff19SB-opc && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/gms-ff14SB && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/mcpb/ezaff-ff14SB && ./Run.pymsmt diffing 1A5T_small.pdb.save with 1A5T_small.pdb PASSED ============================================================== diffing 1A5T_small_opt.com.save with 1A5T_small_opt.com PASSED ============================================================== diffing 1A5T_small_opt.inp.save with 1A5T_small_opt.inp PASSED ============================================================== diffing 1A5T_small_fc.inp.save with 1A5T_small_fc.inp PASSED ============================================================== diffing 1A5T_small_fc.com.save with 1A5T_small_fc.com PASSED ============================================================== diffing 1A5T_standard.pdb.save with 1A5T_standard.pdb PASSED ============================================================== diffing 1A5T_standard.fingerprint.save with 1A5T_standard.fingerprint PASSED ============================================================== diffing 1A5T_large_mk.inp.save with 1A5T_large_mk.inp PASSED ============================================================== diffing 1A5T_large_mk.com.save with 1A5T_large_mk.com PASSED ============================================================== diffing 1A5T_large.pdb.save with 1A5T_large.pdb PASSED ============================================================== diffing 1A5T_large.fingerprint.save with 1A5T_large.fingerprint PASSED ============================================================== diffing 1A5T_mcpbpy_pre.frcmod.save with 1A5T_mcpbpy_pre.frcmod PASSED ============================================================== diffing 1A5T_mcpbpy.frcmod.save with 1A5T_mcpbpy.frcmod PASSED ============================================================== diffing resp1.in.save with resp1.in PASSED ============================================================== diffing resp2.in.save with resp2.in PASSED ============================================================== diffing ZN1.mol2.save with ZN1.mol2 PASSED ============================================================== diffing CM4.mol2.save with CM4.mol2 PASSED ============================================================== diffing CM3.mol2.save with CM3.mol2 PASSED ============================================================== diffing CM2.mol2.save with CM2.mol2 PASSED ============================================================== diffing CM1.mol2.save with CM1.mol2 PASSED ============================================================== diffing 1A5T_mcpbpy.pdb.save with 1A5T_mcpbpy.pdb PASSED ============================================================== diffing 1A5T_tleap.in.save with 1A5T_tleap.in PASSED ============================================================== diffing 1A5T_dry.prmtop.save with 1A5T_dry.prmtop PASSED ============================================================== diffing 1A5T_dry.inpcrd.save with 1A5T_dry.inpcrd PASSED ============================================================== diffing 1A5T_dry.pdb.save with 1A5T_dry.pdb PASSED ============================================================== diffing 1A5T_solv.prmtop.save with 1A5T_solv.prmtop PASSED ============================================================== diffing 1A5T_solv.inpcrd.save with 1A5T_solv.inpcrd PASSED ============================================================== diffing 1A5T_solv.pdb.save with 1A5T_solv.pdb PASSED ============================================================== cd pymsmt/pdbsearcher && ./Run.pymsmt diffing 2MXV_res_691_MetalCenter.pdb.save with 2MXV_res_691_MetalCenter.pdb PASSED ============================================================== diffing 5AHO_res_2547_MetalCenter.pdb.save with 5AHO_res_2547_MetalCenter.pdb PASSED ============================================================== diffing 5AHO_res_2548_MetalCenter.pdb.save with 5AHO_res_2548_MetalCenter.pdb PASSED ============================================================== diffing Zn_env.csv.save with Zn_env.csv PASSED ============================================================== diffing Zn_sum.csv.save with Zn_sum.csv PASSED ============================================================== cd pymsmt/amb2chm_psf && ./Run.pymsmt diffing 1OKL_solv.psf.save with 1OKL_solv.psf PASSED ============================================================== diffing 1OKL_solv.crd.save with 1OKL_solv.crd PASSED ============================================================== diffing 1OKL_solv.charmm.pdb.save with 1OKL_solv.charmm.pdb PASSED ============================================================== cd pymsmt/amb2chm_par && ./Run.pymsmt diffing MNS.frcmod.save with MNS.frcmod PASSED ============================================================== diffing MNS_new_attyp.frcmod.save with MNS_new_attyp.frcmod PASSED ============================================================== diffing parmff14SB_1okl.prm.save with parmff14SB_1okl.prm PASSED ============================================================== cd pymsmt/amb2gro && ./Run.pymsmt diffing 1OKL_solv.top.truc.save with 1OKL_solv.top.truc PASSED ============================================================== diffing 1OKL_solv.gro.save with 1OKL_solv.gro PASSED ============================================================== diffing 1OKL_solv.gromacs.pdb.save with 1OKL_solv.gromacs.pdb PASSED ============================================================== cd pymsmt/pdb2mol2 && ./Run.pymsmt diffing ZN.mol2.save with ZN.mol2 PASSED ============================================================== cd packmol_memgen/ && ./Run.packmol-memgen running memembed PASSED ============================================================== running simple packmol-memgen run PASSED ============================================================== cd mmpbsa_py && make test make[3]: Entering directory '/usr/local/amber22/AmberTools/test/mmpbsa_py' ./Run.exist diffing mmpbsa.out.save with mmpbsa.out PASSED ============================================================== cd EstRAL_Files && ./Run.makeparms diffing com.top with c.top PASSED ============================================================== diffing rec.top with r.top PASSED ============================================================== diffing lig.top with l.top PASSED ============================================================== cd 01_Generalized_Born && ./Run.GB diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing energies.csv.save with energies.csv PASSED ============================================================== cd 02_Poisson_Boltzmann && ./Run.PB diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing energies.csv.save with energies.csv PASSED ============================================================== cd 03_Alanine_Scanning && ./Run.ALA diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing orig_mutant.mdcrd with _MMPBSA_mutant_complex.mdcrd.0 PASSED ============================================================== cd 10_QM_MMGBSA && ./Run.QMMMGBSA diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== cd 11_3D-RISM && ./Run.rism3d diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== cd 12_Membrane_Channel && ./Run.mem diffing FINAL_RESULTS_AMI.dat.save with FINAL_RESULTS_AMI.dat PASSED ============================================================== diffing energies.csv.save with energies.csv PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/AmberTools/test/mmpbsa_py' cd bar_pbsa && ./Run.bar_pbsa Running BAR/PBSA with 1 threads Skipping complex runs with 1 threads ./Run.bar_pbsa: 31: [[: not found Missing modules All tests skipped make[2]: Leaving directory '/usr/local/amber22/AmberTools/test' make[2]: Entering directory '/usr/local/amber22/test' cd dmp && ./Run.dmp diffing mdout.dmp.save with mdout.dmp PASSED ============================================================== cd adenine && ./Run.adenine diffing mdout.adenine.save with mdout.adenine PASSED ============================================================== cd variable_14 && ./Run.variable_14_igb1 diffing variable_14_igb1.mdout.save with variable_14_igb1.mdout PASSED ============================================================== cd rdc && ./Run.nef diffing 1pqx.RST.save with 1pqx.RST PASSED ============================================================== cd cytosine && ./Run.cytosine diffing cytosine.out.save with cytosine.out PASSED ============================================================== cd nonper && ./Run.nonper diffing mdout.nonper.save with mdout.nonper PASSED ============================================================== cd nonper && ./Run.egb6 diffing mdout.egb6.save with mdout.egb6 PASSED ============================================================== cd nonper && ./Run.nonper.belly diffing mdout.belly.save with mdout.belly PASSED ============================================================== cd nonper && ./Run.nonper.belly.mask diffing mdout.belly.mask.save with mdout.belly.mask PASSED ============================================================== cd nonper && ./Run.nonper.min diffing mdout.min.save with mdout.min PASSED ============================================================== cd nonper && ./Run.cap diffing mdout.cap.save with mdout.cap PASSED ============================================================== cd nonper && ./Run.nonper.nocut diffing mdout.nocut.save with mdout.nocut PASSED ============================================================== cd tip4p && ./Run.tip4p diffing mdout.tip4p.save with mdout.tip4p PASSED ============================================================== cd tip4p && ./Run.tip4p_mcbar diffing mdout.mcbar.tip4p.sander.save with mdout.mcbar.tip4p.sander PASSED ============================================================== diffing mdout.mcbar_aniso.tip4p.sander.save with mdout.mcbar_aniso.tip4p.sander PASSED ============================================================== cd tip4p && ./Run.tip4p_nve diffing mdout.tip4p_nve.save with mdout.tip4p_nve PASSED ============================================================== cd tip5p && ./Run.tip5p diffing mdout.tip5p.save with mdout.tip5p PASSED ============================================================== cd tip5p && ./Run.tip5p_nve diffing mdout.tip5p_nve.save with mdout.tip5p_nve PASSED ============================================================== cd 4096wat && ./Run.pure_wat diffing mdout.pure_wat.save with mdout.pure_wat PASSED ============================================================== cd 4096wat && ./Run.pure_wat_fswitch diffing mdout.pure_wat_fswitch.save with mdout.pure_wat_fswitch PASSED ============================================================== cd 4096wat && ./Run.pure_wat_nmr_temp_reg diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp PASSED ============================================================== cd 4096wat && ./Run.vrand diffing mdout.vrand.save with mdout.vrand PASSED ============================================================== cd 4096wat && ./Run.frcdmp diffing mdout.pure_wat2.save with mdout.pure_wat2 PASSED ============================================================== diffing mdfrc_cmp.save with mdfrc_cmp PASSED ============================================================== cd 4096wat_oct && ./Run.pure_wat_oct diffing mdout.pure_wat_oct.save with mdout.pure_wat_oct PASSED ============================================================== diffing mdcrd.pure_wat_oct.save with mdcrd.pure_wat_oct PASSED ============================================================== cd dhfr && ./Run.dhfr && ./Run.dhfr prmtop_an diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== cd dhfr && ./Run.dhfr.noboxinfo diffing mdout.dhfr.noboxinfo.save with mdout.dhfr.noboxinfo PASSED ============================================================== cd dhfr && ./Run.dhfr.noshake diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake PASSED ============================================================== cd dhfr && ./Run.dhfr.ntx diffing mdout.dhfr.ntx.save with mdout.dhfr.ntx PASSED ============================================================== cd dhfr && ./Run.dhfr.bussi diffing mdout.dhfr.bussi.save with mdout.dhfr.bussi PASSED ============================================================== cd dhfr && ./Run.dhfr.min diffing mdout.dhfr.min.save with mdout.dhfr.min PASSED ============================================================== cd dhfr && ./Run.dhfr.min_prcg diffing mdout.dhfr.min_prcg.save with mdout.dhfr.min_prcg PASSED ============================================================== cd dhfr && ./Run.dhfr.xmin diffing mdout.dhfr.xmin.save with mdout.dhfr.xmin PASSED ============================================================== cd ff14ipq && ./Run.ff14ipq diffing mdout.ff14ipq.save with mdout.ff14ipq PASSED ============================================================== cd variable_14 && ./Run.variable_14_ntb1 diffing variable_14_ntb1.mdout.save with variable_14_ntb1.mdout PASSED ============================================================== cd gact_ips && ./Run.ips diffing mdout.ips.save with mdout.ips PASSED ============================================================== cd gact_ips && ./Run.ipsnve diffing mdout.ipsnve.save with mdout.ipsnve PASSED ============================================================== cd gact_ips && ./Run.ips_dfft diffing mdout.ips_dfft.save with mdout.ips_dfft PASSED ============================================================== cd gact_ips && ./Run.ips_vacuum diffing mdout.ips_vacuum.save with mdout.ips_vacuum PASSED ============================================================== cd polarizable_water && ./Run.pol_wat diffing mdout.polwat.save with mdout.polwat PASSED ============================================================== cd ubiquitin && ./Run.ubiquitin diffing mdout.ubiquitin.save with mdout.ubiquitin PASSED ============================================================== diffing mden.save with mden PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== cd dna_pol && ./Run.dna_pol diffing mdout.dna_pol.save with mdout.dna_pol PASSED ============================================================== cd trx && ./Run.trx diffing mdout.trx.save with mdout.trx PASSED ============================================================== cd trx && ./Run.trx.cpln diffing mdout.trx.cpln.save with mdout.trx.cpln PASSED ============================================================== cd rdc && ./Run.dip diffing gcg.dip.o.save with gcg.dip.o PASSED ============================================================== cd rdc && ./Run.csa diffing gcg.csa.o.save with gcg.csa.o PASSED ============================================================== cd rdc && ./Run.csa_min diffing gcg.csa_min.o.save with gcg.csa_min.o PASSED ============================================================== cd rdc && ./Run.nmr diffing gcg.nmr.o.save with gcg.nmr.o PASSED ============================================================== cd pcsa && ./Run.dip diffing stem.dip.o.save with stem.dip.o PASSED ============================================================== cd pcsa && ./Run.csa diffing stem.csa.o.save with stem.csa.o PASSED ============================================================== cd pcsa && ./Run.csa2 diffing stem.csa2.o.save with stem.csa2.o PASSED ============================================================== cd pcsa && ./Run.csa_min diffing stem.csa_min.o.save with stem.csa_min.o PASSED ============================================================== cd tgtmd/change_target && ./Run.tgtmd diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.rms && ./Run.tgtmd diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.ntr && ./Run.tgtmd diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/conserve_ene && ./Run.tgtmd diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/minimize && ./Run.tgtmin diffing tgtmin.out.save with tgtmin.out PASSED ============================================================== cd tgtmd/PME && ./Run.tgtPME diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd mtmdtest && ./Run.mtmdtest SANDER: Multiply-targeted MD, new to AMBER 11 Tested on an RNA duplex. diffing mtmdtest.out.save with mtmdtest.out PASSED ============================================================== diffing mtmdtest.mdcrd.save with mtmdtest.mdcrd PASSED ============================================================== cd trajene && ./Run.trajene diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.save with mdcrd.out PASSED ============================================================== diffing mdfrc.out.save with mdfrc.out PASSED ============================================================== cd trajene_box && ./Run.trajene diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.save with mdcrd.out PASSED ============================================================== cd trajene_netcdf && ./Run.trajene yes diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.nc.save with mdcrd.out.nc PASSED ============================================================== cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== cd umbrella && ./Run.umbrella diffing mdout.umbrella.save with mdout.umbrella PASSED ============================================================== diffing chi_vs_t.save with chi_vs_t PASSED ============================================================== cd noesy && ./Run.noesy diffing noesy.out.save with noesy.out PASSED ============================================================== cd jar && ./Run.jarz diffing mdout.jar.save with mdout.jar PASSED ============================================================== diffing dist_vs_t.save with dist_vs_t PASSED ============================================================== cd plane_plane_restraint && ./Run.dinuc_plpt SANDER: Dinucleoside restrained with new plane-point angle restraint that was defined with new natural language restraint input. diffing mdout.dinucAU_plpt.save with mdout.dinucAU_plpt PASSED ============================================================== diffing dinuc_plpt_vs_t.save with dinuc_plpt_vs_t PASSED ============================================================== cd plane_plane_restraint && ./Run.dinuc_pln SANDER: Dinucleoside restrained with new plane-plane angle restraint that was defined with new natural language restraint input. diffing mdout.dinucAU_pln.save with mdout.dinucAU_pln PASSED ============================================================== diffing dinuc_pln_vs_t.save with dinuc_pln_vs_t PASSED ============================================================== cd iwrap2 && ./Run.iwrap2 diffing mdout.iw2.save with mdout.iw2 PASSED ============================================================== diffing mdcrd.iw2.save with mdcrd.iw2 PASSED ============================================================== diffing rstrt.iw2.save with rstrt.iw2 PASSED ============================================================== cd idecomp1 && ./run_idecomp1.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd idecomp4 && ./run_idecomp4.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd bintraj && ./Run.bintraj yes diffing nc_headers.save with nc_headers PASSED ============================================================== cd netcdf && make -k test OPT=yes make[3]: Entering directory '/usr/local/amber22/test/netcdf' Netcdf MD Restart Write Test diffing textmd.rst7.save with textmd.rst7 PASSED ============================================================== Netcdf Minimization Restart Write Test diffing textmin.rst7.save with textmin.rst7 PASSED ============================================================== Restrained MD with netcdf Restart Reference Coords Test diffing md.rst7.save with md.rst7 PASSED ============================================================== diffing ene.dat.save with ene.dat PASSED ============================================================== Netcdf MD restart read test, ntx=5 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== Netcdf MD restart read test, ntx=1 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/test/netcdf' cd velocity_write && ./Run.vel1 diffing vel1.vel.save with vel1.vel PASSED ============================================================== diffing vel1.crd.save with vel1.crd PASSED ============================================================== diffing vel1.frc.save with vel1.frc PASSED ============================================================== cd velocity_write && ./Run.vel2 diffing vel2.vel.save with vel2.vel PASSED ============================================================== diffing vel1.crd.save with vel2.crd PASSED ============================================================== diffing vel1.frc.save with vel2.frc PASSED ============================================================== cd csurften && ./Run.csurften_z-dir diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir PASSED ============================================================== cd csurften && ./Run.csurften_z-dir_npt_3 diffing mdout.csurften_z-dir_npt_3.save with mdout.csurften_z-dir_npt_3 PASSED ============================================================== cd linear_interaction_energy && ./Run.lie diffing mdout.lie.save with mdout.lie PASSED ============================================================== cd nmropt && make all make[3]: Entering directory '/usr/local/amber22/test/nmropt' cd gb/angle && ./Run.nmropt_1angle_gb diffing mdout.save with mdout PASSED ============================================================== diffing angle_gb_vs_t.save with angle_gb_vs_t PASSED ============================================================== cd gb/distance && ./Run.dist_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/distance_COM && ./Run.distCOM_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_distance && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/jar_distance_COM && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_gb.dat.save with jartorsion_gb.dat PASSED ============================================================== cd gb/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_gb.dat.save with torsion_gb.dat PASSED ============================================================== cd gb/tautp && ./Run.nmropt_1tautp_gb diffing mdout.save with mdout PASSED ============================================================== cd gb/temp && ./Run.nmropt_1temp_gb diffing mdout.save with mdout PASSED ============================================================== cd gb/angle_torsion_com/ && ./Run.angdihCOM_gb diffing mdout.save with mdout PASSED ============================================================== diffing angtorCOM_gb.save with angtorCOM_gb PASSED ============================================================== cd pme/angle && ./Run.nmropt_1angle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing angle_pbc_vs_t.save with angle_pbc_vs_t PASSED ============================================================== cd pme/distance && ./Run.dist_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/distance_COM && ./Run.distCOM_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_pbc.dat.save with jartorsion_pbc.dat PASSED ============================================================== cd pme/jar_distance && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/jar_distance_COM && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_pbc.dat.save with torsion_pbc.dat PASSED ============================================================== cd pme/tautp && ./Run.nmropt_1tautp_pbc diffing mdout.save with mdout PASSED ============================================================== cd pme/temp && ./Run.nmropt_1temp_pbc diffing mdout.save with mdout PASSED ============================================================== cd pme/angle_torsion_com/ && ./Run.angdihCOM diffing mdout.save with mdout PASSED ============================================================== diffing angtorCOM.save with angtorCOM PASSED ============================================================== cd gb/2xangle && ./Run.nmropt_1_2xangle_gb diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_gb_vs_t.save with 2xangle_gb_vs_t PASSED ============================================================== cd gb/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_gb.dat.save with jartorsion_com_gb.dat PASSED ============================================================== cd gb/jar_lcod && ./Run.lcod_jar diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/jar_lcod_dist && ./Run.jar_lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod && ./Run.lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_gb.dat.save with 2xtorsion_gb.dat PASSED ============================================================== cd pme/2xangle && ./Run.nmropt_1_2xangle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_pbc_vs_t.save with 2xangle_pbc_vs_t PASSED ============================================================== cd pme/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_pbc.dat.save with jartorsion_com_pbc.dat PASSED ============================================================== cd pme/jar_lcod && ./Run.jar_lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/jar_lcod_dist && ./Run.lcod_dist diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod && ./Run.lcod_pme diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_pbc.dat.save with 2xtorsion_pbc.dat PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/test/nmropt' cd lj_12-6-4 && ./Run.12-6-4 diffing mdout.save with mdout PASSED ============================================================== cd baroscalingdir && ./Run.baroscalingdir_z-dir diffing mdout.baroscalingdir_z-dir.sander.save with mdout.baroscalingdir_z-dir PASSED ============================================================== cd ff19SB && ./Run.sander diffing mdout.save.sander with mdout PASSED ============================================================== cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== cd gb_rna && ./Run.gbrna.ips diffing mdout.gbrna.ips.save with mdout.gbrna.ips PASSED ============================================================== cd gbsa_xfin && ./Run.gbsa1 diffing mdout.gbsa1.save with mdout.gbsa1 PASSED ============================================================== cd circ_dna && ./Run.circdna diffing mdout.circdna.save with mdout.circdna PASSED ============================================================== cd gb2_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb7_trx && ./Run.trxox && ./Run.trxox prmtop_an diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb7_trx && ./Run.trxox_md diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== cd gb8_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb8_trx && ./Run.trxox_md && ./Run.trxox_md prmtop_an diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== cd gbneck2nu/1hji && ./Run.1hji_md diffing mdout.1hji_md.save with mdout.1hji_md PASSED ============================================================== cd gbneck2nu/modified_nu/3p4a/ && ./Run.3p4a diffing mdout.3p4a.save with mdout.3p4a PASSED ============================================================== cd alpb_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd LES_noPME && ./Run.LESmd SANDER: LES MD gas phase diffing md.out.save with md.out PASSED ============================================================== cd LES_noPME && ./Run.LESmd.rdiel SANDER: LES MD gas phase rdiel diffing md.rdiel.out.save with md.rdiel.out PASSED ============================================================== cd LES && ./Run.PME_LES ADDLES and SANDER.LES test: addles: diffing output_addles.save with output_addles PASSED ============================================================== diffing LES.crd.save with LES.crd PASSED ============================================================== diffing LES.prmtop.save with LES.prmtop PASSED ============================================================== sander.LES: diffing md.LES.out.save with md.LES.out PASSED ============================================================== cd LES_CUT && ./Run.LES SANDER.LES test, no PME diffing md.LES.out.save with md.LES.out PASSED ============================================================== cd LES_TEMP && ./Run.2temp SANDER: LES T coupling diffing 2temp.out.save with 2temp.out PASSED ============================================================== cd LES_GB && ./Run.LES SANDER: LES+GB 1: GB/LES GB1 diffcoords diffing les.gb1.diffcrd.out.save with les.gb1.diffcrd.out PASSED ============================================================== 1: GB/LES GB1 samecoords diffing les.gb1.samecrd.out.save with les.gb1.samecrd.out PASSED ============================================================== 1: GB/LES GB5 samecoords diffing les.gb5.samecrd.out.save with les.gb5.samecrd.out PASSED ============================================================== 1: GB/LES GB7 samecoords diffing les.gb7.samecrd.out.save with les.gb7.samecrd.out PASSED ============================================================== 1: GB/LES GB7 diffcoords w/RDT diffing les.gb7.rdt.out.save with les.gb7.rdt.out PASSED ============================================================== cd PIMD/part_pimd_water && ./Run.pimd diffing addles.out.save with addles.out PASSED ============================================================== diffing pimd.out.save with pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_water && ./Run.nmpimd diffing nmpimd.out.save with nmpimd.out PASSED ============================================================== cd PIMD/part_pimd_helium && ./Run.pimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_helium && ./Run.nmpimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_ntp && ./Run.nmpimd diffing ntp_nmpimd.out.save with ntp_nmpimd.out PASSED ============================================================== diffing NHC.dat.save with NHC.dat PASSED ============================================================== cd PIMD/part_pimd_spcfw && ./Run.pimd diffing spcfw_pimd.top.save with spcfw_pimd.top PASSED ============================================================== diffing spcfw_pimd.xyz.save with spcfw_pimd.xyz PASSED ============================================================== diffing spcfw_pimd.out.save with spcfw_pimd.out PASSED ============================================================== cd PIMD/part_rpmd_water && ./Run.rpmd diffing spcfw_rpmd.top.save with spcfw_rpmd.top PASSED ============================================================== diffing spcfw_rpmd.xyz.save with spcfw_rpmd.xyz PASSED ============================================================== diffing spcfw_rpmd.out.save with spcfw_rpmd.out PASSED ============================================================== cd ti_mass/pent_LES_PIMD && ./Run.pentadiene diffing addles.out.save with addles.out PASSED ============================================================== diffing pent-TI_les.top.save with pent-TI_les.top PASSED ============================================================== diffing pimd.out.save with pimd.out PASSED ============================================================== cd nfe && ./run-serial.sh >>>>>>> doing 'abmd_ANALYSIS' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/monitor.txt with monitor.txt PASSED ============================================================== >>>>>>> doing 'abmd_FLOODING' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/monitor.txt with monitor.txt PASSED ============================================================== diffing umbrella.save.ncdump with umbrella.ncdump PASSED ============================================================== diffing wt_umbrella.save.ncdump with wt_umbrella.ncdump PASSED ============================================================== >>>>>>> doing 'abmd_UMBRELLA' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/monitor.txt with monitor.txt PASSED ============================================================== >>>>>>> doing 'smd' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/smd.txt with smd.txt PASSED ============================================================== >>>>>>> doing 'pmd' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/pmd.txt with pmd.txt PASSED ============================================================== >>>>>>> doing 'smd2' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/work.txt with work.txt PASSED ============================================================== cd pgm_512wat && ./Run.nve diffing nve.out.save with nve.out possible FAILURE: check nve.out.dif ============================================================== cd sander_pbsa_dmp && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== cd sander_pbsa_ipb2 && ./Run.110D.min diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== cd sander_pbsa_delphi && ./Run.1az6.min diffing mdout.1az6.min.save with mdout.1az6.min PASSED ============================================================== cd sander_pbsa_lpb && ./Run.lsolver.min bcoption=5 solvopt=1 diffing out.save/mdout.min_bc5_solv1.save with mdout.min_bc5_solv1 PASSED ============================================================== bcoption=5 solvopt=2 diffing out.save/mdout.min_bc5_solv2.save with mdout.min_bc5_solv2 PASSED ============================================================== bcoption=5 solvopt=3 diffing out.save/mdout.min_bc5_solv3.save with mdout.min_bc5_solv3 PASSED ============================================================== bcoption=5 solvopt=4 diffing out.save/mdout.min_bc5_solv4.save with mdout.min_bc5_solv4 PASSED ============================================================== bcoption=6 solvopt=1 diffing out.save/mdout.min_bc6_solv1.save with mdout.min_bc6_solv1 PASSED ============================================================== bcoption=6 solvopt=3 diffing out.save/mdout.min_bc6_solv3.save with mdout.min_bc6_solv3 PASSED ============================================================== bcoption=6 solvopt=4 diffing out.save/mdout.min_bc6_solv4.save with mdout.min_bc6_solv4 PASSED ============================================================== cd sander_pbsa_radi && ./Run.ion.min diffing ./out.save/Na.inp1.out.save with Na.inp1.out PASSED ============================================================== diffing ./out.save/Na.inp2.out.save with Na.inp2.out PASSED ============================================================== diffing ./out.save/nma.inp1.out.save with nma.inp1.out PASSED ============================================================== diffing ./out.save/nma.inp2.out.save with nma.inp2.out PASSED ============================================================== diffing ./out.save/da.inp1.out.save with da.inp1.out PASSED ============================================================== diffing ./out.save/da.inp2.out.save with da.inp2.out PASSED ============================================================== cd sander_pbsa_tsr && ./Run.tsrb.min diffing mdout.tsrb.min.save with mdout.tsrb.min PASSED ============================================================== cd sander_pbsa_frc && ./test dbf_0.argasp checking argasp force diffing force.save with force.dat PASSED ============================================================== dbf_0.dadt checking dadt force diffing force.save with force.dat PASSED ============================================================== dbf_0.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_0.lysasp checking lysasp force diffing force.save with force.dat PASSED ============================================================== dbf_0.polyALA checking polyALA force diffing force.save with force.dat PASSED ============================================================== dbf_0.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_1.argasp checking argasp force diffing force.save with force.dat PASSED ============================================================== dbf_1.dadt checking dadt force diffing force.save with force.dat PASSED ============================================================== dbf_1.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_1.lysasp checking lysasp force diffing force.save with force.dat PASSED ============================================================== dbf_1.polyALA checking polyALA force diffing force.save with force.dat PASSED ============================================================== dbf_1.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_2.argasp checking argasp force diffing force.save with force.dat PASSED ============================================================== dbf_2.dadt checking dadt force diffing force.save with force.dat PASSED ============================================================== dbf_2.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_2.lysasp checking lysasp force diffing force.save with force.dat PASSED ============================================================== dbf_2.polyALA checking polyALA force diffing force.save with force.dat PASSED ============================================================== dbf_2.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_4.420D checking 420D force diffing force.save with force.dat PASSED ============================================================== dbf_4.1F81 checking 1F81 force diffing force.save with force.dat PASSED ============================================================== cd sander_pbsa_decres && ./Run.pbsa_decres diffing mdout.pbsa_decres.save with mdout.pbsa_decres PASSED ============================================================== cd sander_pbsa_decpw && ./Run.pbsa_decpw diffing mdout.pbsa_decpw.save with mdout.pbsa_decpw PASSED ============================================================== cd sander_pbsa_ligand && ./Run diffing mdout.lig.min.save with mdout.lig.min PASSED ============================================================== cd sander_pbsa_imin5 && ./Run.min diffing minout.save with minout PASSED ============================================================== cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== cd cnstph/explicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== cd cnste/implicit && ./Run.cnste diffing mdout.save with mdout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== cd cnste/explicit && ./Run.cnste diffing mdout.save with mdout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== cd cnstphe/implicit && ./Run.cnstphe diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== cd cnstphe/explicit && ./Run.cnstphe diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== cd cnstphe_merged/implicit && ./Run.cnstphe diffing mdout.save with mdout PASSED ============================================================== diffing cpeout.save with cpeout PASSED ============================================================== cd cnstphe_merged/explicit && ./Run.cnstphe diffing mdout.save with mdout PASSED ============================================================== diffing cpeout.save with cpeout PASSED ============================================================== cd rism3d/ala && ./Run.ala diffing ala.np0.out.save.totChg with ala.np0.out.totChg PASSED ============================================================== diffing ala.np0.out.save.rel with ala.np0.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.mdiis0 diffing ala.mdiis0.out.save.totChg with ala.mdiis0.out.totChg PASSED ============================================================== diffing ala.mdiis0.out.save.rel with ala.mdiis0.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.mdiis1 diffing ala.mdiis1.out.save.totChg with ala.mdiis1.out.totChg PASSED ============================================================== diffing ala.mdiis1.out.save.rel with ala.mdiis1.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.dist diffing ala.dist.out.save with ala.dist.out PASSED ============================================================== diffing guv.O.5.dx.save with guv.O.5.dx PASSED ============================================================== diffing huv.H1.5.dx.save with huv.H1.5.dx PASSED ============================================================== diffing guv_dT.O.5.dx.save with guv_dT.O.5.dx PASSED ============================================================== diffing guv_dT.H1.5.dx.save with guv_dT.H1.5.dx PASSED ============================================================== diffing uuv.O.5.dx.save with uuv.O.5.dx PASSED ============================================================== diffing uuv.H1.5.dx.save with uuv.H1.5.dx PASSED ============================================================== diffing cuv_dT.O.5.dx.save with cuv_dT.O.5.dx PASSED ============================================================== diffing cuv_dT.H1.5.dx.save with cuv_dT.H1.5.dx PASSED ============================================================== diffing asympcr.5.dx.save with asympcr.5.dx PASSED ============================================================== diffing quv.5.dx.save with quv.5.dx PASSED ============================================================== diffing chgdist.5.dx.save with chgdist.5.dx PASSED ============================================================== diffing exchem.5.dx.save with exchem.5.dx PASSED ============================================================== diffing exchem.mol.5.dx.save with exchem.mol.5.dx PASSED ============================================================== diffing exchem.O.5.dx.save with exchem.O.5.dx PASSED ============================================================== diffing exchem.H1.5.dx.save with exchem.H1.5.dx PASSED ============================================================== diffing solvene.5.dx.save with solvene.5.dx PASSED ============================================================== diffing solvene.mol.5.dx.save with solvene.mol.5.dx PASSED ============================================================== diffing solvene.O.5.dx.save with solvene.O.5.dx PASSED ============================================================== diffing solvene.H1.5.dx.save with solvene.H1.5.dx PASSED ============================================================== diffing entropy.5.dx.save with entropy.5.dx PASSED ============================================================== diffing entropy.mol.5.dx.save with entropy.mol.5.dx PASSED ============================================================== diffing entropy.O.5.dx.save with entropy.O.5.dx PASSED ============================================================== diffing entropy.H1.5.dx.save with entropy.H1.5.dx PASSED ============================================================== diffing exchemGF.5.dx.save with exchemGF.5.dx PASSED ============================================================== diffing exchemGF.O.5.dx.save with exchemGF.O.5.dx PASSED ============================================================== diffing exchemGF.H1.5.dx.save with exchemGF.H1.5.dx PASSED ============================================================== diffing solveneGF.5.dx.save with solveneGF.5.dx PASSED ============================================================== diffing solveneGF.O.5.dx.save with solveneGF.O.5.dx PASSED ============================================================== diffing solveneGF.H1.5.dx.save with solveneGF.H1.5.dx PASSED ============================================================== diffing entropyGF.5.dx.save with entropyGF.5.dx PASSED ============================================================== diffing entropyGF.O.5.dx.save with entropyGF.O.5.dx PASSED ============================================================== diffing entropyGF.H1.5.dx.save with entropyGF.H1.5.dx PASSED ============================================================== diffing potUV.5.dx.save with potUV.5.dx PASSED ============================================================== diffing potUV.mol.5.dx.save with potUV.mol.5.dx PASSED ============================================================== diffing potUV.O.5.dx.save with potUV.O.5.dx PASSED ============================================================== diffing potUV.H1.5.dx.save with potUV.H1.5.dx PASSED ============================================================== cd rism3d/ala && ./Run.ala.dist.xyzv diffing quv.5.xyzv.trunc.save with quv.5.xyzv.trunc PASSED ============================================================== cd rism3d/ala && ./Run.ala.hnc diffing ala.hnc.out.save.totChg with ala.hnc.out.totChg PASSED ============================================================== diffing ala.hnc.out.save.rel with ala.hnc.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.list diffing ala.list.out.save.totChg with ala.list.out.totChg PASSED ============================================================== diffing ala.list.out.save.rel with ala.list.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.imin5 diffing ala.imin5.out.save.totChg with ala.imin5.out.totChg PASSED ============================================================== diffing ala.imin5.out.save.rel with ala.imin5.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.resize.fast diffing ala.resize.fast.out.save.totChg with ala.resize.fast.out.totChg PASSED ============================================================== diffing ala.resize.fast.out.save.rel with ala.resize.fast.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.tree.fast diffing ala.tree.fast.out.save.totChg with ala.tree.fast.out.totChg PASSED ============================================================== diffing ala.tree.fast.out.save.rel with ala.tree.fast.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.nacl.fast diffing ala.nacl.fast.out.save.totChg with ala.nacl.fast.out.totChg PASSED ============================================================== diffing ala.nacl.fast.out.save.rel with ala.nacl.fast.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.nacl.tree.fast diffing ala.nacl.tree.fast.out.save.totChg with ala.nacl.tree.fast.out.totChg PASSED ============================================================== diffing ala.nacl.tree.fast.out.save.rel with ala.nacl.tree.fast.out.rel PASSED ============================================================== cd rism3d/ala && ./Run.ala.min.fast diffing ala.min.fast.out.save.totChg with ala.min.fast.out.totChg PASSED ============================================================== diffing ala.min.fast.out.save.rel with ala.min.fast.out.rel PASSED ============================================================== cd rism3d/phosphate && ./Run.ph1 diffing ph1.out.save.totChg with ph1.out.totChg PASSED ============================================================== diffing ph1.out.save.rel with ph1.out.rel PASSED ============================================================== cd rism3d/phosphate && ./Run.ph1.pse3 diffing ph1.pse3.out.save.totChg with ph1.pse3.out.totChg PASSED ============================================================== diffing ph1.pse3.out.save.rel with ph1.pse3.out.rel PASSED ============================================================== cd rism3d/phosphate && ./Run.ph1-nacl diffing ph1-nacl.out.save.totChg with ph1-nacl.out.totChg PASSED ============================================================== diffing ph1-nacl.out.save.rel with ph1-nacl.out.rel PASSED ============================================================== cd rism3d/phosphate && ./Run.ph1-nacl.pse3 diffing ph1-nacl.pse3.out.save.totChg with ph1-nacl.pse3.out.totChg PASSED ============================================================== diffing ph1-nacl.pse3.out.save.rel with ph1-nacl.pse3.out.rel PASSED ============================================================== cd rism3d/1ahoa && ./Run.1ahoa.pme SANDER: 3D-RISM: PME potential - orthorhombic diffing erism.pme.out.save with erism.pme.out PASSED ============================================================== cd rism3d/4lzt && ./Run.4lzt.pme SANDER: 3D-RISM: PME potential - triclinic diffing erism.out.save with erism.out PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; unset DO_PARALLEL; cd ../AmberTools/test/kmmd/kmmd_sander && ./Run.kmmd running: /usr/local/amber22///bin/sander diffing mdout.save with mdout PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; unset DO_PARALLEL; cd ../AmberTools/test/kmmd/kmmd_sander_gb && ./Run.kmmd diffing mdout.save with mdout PASSED ============================================================== (cd crg_reloc/water && ./Run.water.min) diffing min.out.save with min.out PASSED ============================================================== (cd crg_reloc/water && ./Run.water.md) diffing md.out.save with md.out PASSED ============================================================== cd amd && make -k test make[3]: Entering directory '/usr/local/amber22/test/amd' Testing AMD with PME diffing mdout.pme.amd1.save with mdout.pme.amd1 PASSED ============================================================== diffing mdout.pme.amd2.save with mdout.pme.amd2 PASSED ============================================================== diffing mdout.pme.amd3.save with mdout.pme.amd3 PASSED ============================================================== Testing AMD with GB diffing mdout.gb.amd1.save with mdout.gb.amd1 PASSED ============================================================== diffing mdout.gb.amd2.save with mdout.gb.amd2 PASSED ============================================================== diffing mdout.gb.amd3.save with mdout.gb.amd3 PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/test/amd' cd scaledMD && make -k test make[3]: Entering directory '/usr/local/amber22/test/scaledMD' Testing scaledMD with PME diffing mdout.save with mdout PASSED ============================================================== make[3]: Leaving directory '/usr/local/amber22/test/scaledMD' export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgld diffing mdout.ips_sgld.save with mdout.ips_sgld PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgldfp diffing mdout.ips_sgldfp.save with mdout.ips_sgldfp PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgldg diffing mdout.ips_sgldg.save with mdout.ips_sgldg PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgmdg diffing mdout.ips_sgmdg.save with mdout.ips_sgmdg PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgldbd2 diffing mdout.ips_sgldbd2.save with mdout.ips_sgldbd2 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgldbd3 diffing mdout.ips_sgldbd3.save with mdout.ips_sgldbd3 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgmdbd2 diffing mdout.ips_sgmdbd2.save with mdout.ips_sgmdbd2 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gact_ips && ./Run.ips_sgmdbd3 diffing mdout.ips_sgmdbd3.save with mdout.ips_sgmdbd3 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgldg diffing mdout.gbrna.sgldg.save with mdout.gbrna.sgldg PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgmdg diffing mdout.gbrna.sgmdg.save with mdout.gbrna.sgmdg PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgldbd2 diffing mdout.gbrna.sgldbd2.save with mdout.gbrna.sgldbd2 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgldbd3 diffing mdout.gbrna.sgldbd3.save with mdout.gbrna.sgldbd3 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgmdbd2 diffing mdout.gbrna.sgmdbd2.save with mdout.gbrna.sgmdbd2 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd gb_rna && ./Run.gbrna.sgmdbd3 diffing mdout.gbrna.sgmdbd3.save with mdout.gbrna.sgmdbd3 PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd emap/ && ./Run.emap diffing mdout.emap.save with mdout.emap PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; cd emap2/ && ./Run.emap2 diffing emap2.out.save with emap2.out PASSED ============================================================== diffing emap2.x.save with emap2.x PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_OIN && ./Run.sander.OIN diffing mdout.sander.OIN.save with mdout.sander.OIN PASSED ============================================================== cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.min diffing mdout.dhfr_charmm_noshake.min.save with mdout.dhfr_charmm_noshake.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.md diffing mdout.dhfr_charmm_noshake.md.save with mdout.dhfr_charmm_noshake.md PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.md diffing mdout.dhfr_charmm.md.save with mdout.dhfr_charmm.md PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sinr && ./RUN.sander.SINR diffing mdout.sander.SINR.save with mdout.sander.SINR PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_music/ptsurf-12h2o && ./Run.music-energy diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_music/pt-water-gal17 && ./Run.md diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_music/pt-water-vsgal17 && ./Run.md diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_music/gal17-barostat && ./Run.md diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_music/gal17-electrostatics && ./Run.shiCoushoCor diffing mdout.shiCoushoCor.save with mdout.shiCoushoCor PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_music/gal17-electrostatics && ./Run.pme diffing mdout.pme.save with mdout.pme PASSED ============================================================== export TESTsander=/usr/local/amber22///bin/sander; cd sander_music/gal17-electrostatics && ./Run.shiftC diffing mdout.shiftC.save with mdout.shiftC PASSED ============================================================== cd middle-scheme/MD_Unconstr_Langevin_water && ./Run.LGV_LF AMBERHOME is /usr/local/amber22// Testing MD with langevin dynamics diffing md_LGV.out.save with md_LGV.out PASSED ============================================================== cd middle-scheme/MD_Constr_Langevin_water && ./Run.LGV_LF AMBERHOME is /usr/local/amber22// Testing MD with langevin dynamics diffing md_LGV.out.save with md_LGV.out PASSED ============================================================== cd middle-scheme/QMMM_Constr_ALA_Methol && ./Run.qmmm Testing MD with qmmm diffing qmmm.out.save with qmmm.out PASSED ============================================================== cd middle-scheme/4096wat && ./Run.pure_wat_middle_scheme diffing mdout.pure_wat_middle_scheme.save with mdout.pure_wat_middle_scheme PASSED ============================================================== cd middle-scheme/DNA7 && ./Run.DNA_middle_scheme diffing mdout.DNA_middle_scheme.save with mdout.DNA_middle_scheme PASSED ============================================================== cd middle-scheme/ETH && ./Run.ETH_middle_scheme diffing mdout.ETH_middle_scheme.save with mdout.ETH_middle_scheme PASSED ============================================================== cd nmode && ./Run.ala-dipeptide NMODE: find normal modes diffing vibs.out.save with vibs.out PASSED ============================================================== NMODE: find Langevin modes diffing lvibs.out.save with lvibs.out PASSED ============================================================== diffing lmode.head.save with lmode.head PASSED ============================================================== cd nmode && ./Run.ala-dipeptide_rgroup NMODE: find normal modes, with a restraint weighting diffing vibsr.out.save with vibsr.out PASSED ============================================================== cd newton_raph && ./Run.newton_raph diffing nmd_min.out.save with nmd_min.out PASSED ============================================================== cd qmmm2/input_validation && ./Run.invalid_atom_ids diffing invalid_atom_ids.out.save with invalid_atom_ids.out PASSED ============================================================== cd qmmm2/input_validation && ./Run.non_unique_qm_atoms diffing non-unique.out.save with non-unique.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_0 diffing nma_md_diag_routine_0.out.save with nma_md_diag_routine_0.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_2 diffing nma_md_diag_routine_2.out.save with nma_md_diag_routine_2.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_3 diffing nma_md_diag_routine_3.out.save with nma_md_diag_routine_3.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_4 diffing nma_md_diag_routine_4.out.save with nma_md_diag_routine_4.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_5 diffing nma_md_diag_routine_5.out.save with nma_md_diag_routine_5.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_6 diffing nma_md_diag_routine_6.out.save with nma_md_diag_routine_6.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_7 diffing nma_md_diag_routine_7.out.save with nma_md_diag_routine_7.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb0 diffing nma_md_qmgb0.out.save with nma_md_qmgb0.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb1 diffing nma_md_qmgb1.out.save with nma_md_qmgb1.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb2 diffing nma_md_qmgb2.out.save with nma_md_qmgb2.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb2_saltcon diffing nma_md_qmgb2_saltcon.out.save with nma_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb3 diffing nma_md_qmgb3.out.save with nma_md_qmgb3.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_shake && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_tight_p && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_tight_p && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3_08 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3_08 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1 && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1_ADDMM && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1_ADDMM && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_RM1 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_RM1 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_RM1 && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_MNDO && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_MNDO && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_MNDO && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PM6 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PM6 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb0 diffing nma_md_qmgb0.out.save with nma_md_qmgb0.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb2 diffing nma_md_qmgb2.out.save with nma_md_qmgb2.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb2_saltcon diffing nma_md_qmgb2_saltcon.out.save with nma_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/1-2-ethanediol_PM3CARB1 && ./Run.PM3CARB1_md diffing ethanediol_md.out.save with ethanediol_md.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_qmmm_int0 diffing lysine_md_qmmm_int0.out.save with lysine_md_qmmm_int0.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_qmmm_int2 diffing lysine_md_qmmm_int2.out.save with lysine_md_qmmm_int2.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_lnk_dis_neg diffing lysine_md_lnk_dis_neg.out.save with lysine_md_lnk_dis_neg.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_lnk_method2 diffing lysine_md_lnk_method_2.out.save with lysine_md_lnk_method_2.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb0 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb0 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb2 diffing lysine_md_igb2.out.save with lysine_md_igb2.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb5 diffing lysine_md_igb5.out.save with lysine_md_igb5.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb7 diffing lysine_md_igb7.out.save with lysine_md_igb7.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_adjust_q1 diffing lysine_md_adjust_q1.out.save with lysine_md_adjust_q1.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_adjust_q2 diffing lysine_md_adjust_q2.out.save with lysine_md_adjust_q2.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_lnk_dis_neg diffing lysine_md_lnk_dis_neg.out.save with lysine_md_lnk_dis_neg.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2_alpb && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_mulliken && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_mulliken && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine_qmmm diffing lysine_qmmm.out.save with lysine_qmmm.out PASSED ============================================================== cd qmmm2/lysine_AM1 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_AM1 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_MNDO && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_MNDO && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM6 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM6 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/meoh-nh3_PM6-DH+ && ./Run.meoh-nh3 diffing meoh-nh3_opt.out.save with meoh-nh3_opt.out PASSED ============================================================== cd qmmm2/meoh-nh3_PM6-DH+ && ./Run.meoh-nh3_md diffing meoh-nh3_md.out.save with meoh-nh3_md.out PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.water_dimer.x diffing water_dimer.out.save with water_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.ammonia_dimer.x diffing ammonia_dimer.out.save with ammonia_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.formic_acid_dimer.x diffing formic_acid_dimer.out.save with formic_acid_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.water_dimer.x diffing water_dimer.out.save with water_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.ammonia_dimer.x diffing ammonia_dimer.out.save with ammonia_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.formic_acid_dimer.x diffing formic_acid_dimer.out.save with formic_acid_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.methanethiol.x diffing methanethiol_water.out.save with methanethiol_water.out PASSED ============================================================== cd qmmm2/znme2/ && ./Run.min diffing znme2.znb.min.out.save with znme2.znb.min.out PASSED ============================================================== cd qmmm2/znme2/ && ./Run.md diffing znme2.znb.md.out.save with znme2.znb.md.out PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod.min diffing mndod.min.mdout.save with mndod.min.mdout PASSED ============================================================== diffing mndod.min.mdcrd.save with mndod.min.mdcrd PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod.md diffing mndod.md.mdout.save with mndod.md.mdout PASSED ============================================================== diffing mndod.md.mdcrd.save with mndod.md.mdcrd PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod-mm.min diffing mndod-mm.min.mdout.save with mndod-mm.min.mdout PASSED ============================================================== diffing mndod-mm.min.mdcrd.save with mndod-mm.min.mdcrd PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod-mm.md diffing mndod-mm.md.mdout.save with mndod-mm.md.mdout PASSED ============================================================== diffing mndod-mm.md.mdcrd.save with mndod-mm.md.mdcrd PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_imaged diffing mdout.oct_nma_imaged.save with mdout.oct_nma_imaged PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_noimage diffing mdout.oct_nma_noimage.save with mdout.oct_nma_noimage PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0 diffing mdout.ortho_qmewald0.save with mdout.ortho_qmewald0 PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.truncoct_qmewald0 diffing mdout.truncoct_qmewald0.save with mdout.truncoct_qmewald0 PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_calc_mulliken diffing crambin_md_calc_mulliken.out.save with crambin_md_calc_mulliken.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2 diffing crambin_md_qmgb2.out.save with crambin_md_qmgb2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_alpb diffing crambin_md_qmgb2_alpb.out.save with crambin_md_qmgb2_alpb.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq1 diffing crambin_md_qmgb2_aq1.out.save with crambin_md_qmgb2_aq1.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq2 diffing crambin_md_qmgb2_aq2.out.save with crambin_md_qmgb2_aq2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_saltcon diffing crambin_md_qmgb2_saltcon.out.save with crambin_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_internal diffing mdout.1NLN_internal.save with mdout.1NLN_internal PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspev diffing mdout.1NLN_dspev.save with mdout.1NLN_dspev PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevd diffing mdout.1NLN_dspevd.save with mdout.1NLN_dspevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevx diffing mdout.1NLN_dspevx.save with mdout.1NLN_dspevx PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyev diffing mdout.1NLN_dsyev.save with mdout.1NLN_dsyev PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevd diffing mdout.1NLN_dsyevd.save with mdout.1NLN_dsyevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevr diffing mdout.1NLN_dsyevr.save with mdout.1NLN_dsyevr PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_auto diffing mdout.1NLN_auto.save with mdout.1NLN_auto PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_min diffing mdout.1NLN_min.save with mdout.1NLN_min PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1 diffing mdout.1NLN_MD_ntb1.save with mdout.1NLN_MD_ntb1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq1 diffing mdout.1NLN_MD_ntb1_aq1.save with mdout.1NLN_MD_ntb1_aq1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2 diffing mdout.1NLN_MD_ntb1_aq2.save with mdout.1NLN_MD_ntb1_aq2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_mmcorr diffing mdout.1NLN_MD_ntb1_mmcorr.save with mdout.1NLN_MD_ntb1_mmcorr PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_qmewald2 diffing mdout.1NLN_MD_ntb1_qmewald2.save with mdout.1NLN_MD_ntb1_qmewald2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb2 diffing mdout.1NLN_MD_ntb2.save with mdout.1NLN_MD_ntb2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2_NUMER_DERIV diffing mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV.save with mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_dis_neg diffing mdout.1NLN_MD_ntb1_lnk_dis_neg.save with mdout.1NLN_MD_ntb1_lnk_dis_neg PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_method2 diffing mdout.1NLN_MD_ntb1_lnk_method2.save with mdout.1NLN_MD_ntb1_lnk_method2 PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged diffing mdout.notimaged.save with mdout.notimaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md diffing mdout.notimaged_md.save with mdout.notimaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme diffing mdout.notimaged_md_pme.save with mdout.notimaged_md_pme PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald diffing mdout.notimaged_md_pme_qmewald.save with mdout.notimaged_md_pme_qmewald PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald_lowmem diffing mdout.notimaged_md_pme_qmewald_lowmem.save with mdout.notimaged_md_pme_qmewald_lowmem PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged diffing mdout.imaged.save with mdout.imaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged_md diffing mdout.imaged_md.save with mdout.imaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center diffing mdout.img_center.save with mdout.img_center PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_md diffing mdout.img_center_md.save with mdout.img_center_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_bigqmcut_md diffing mdout.img_center_bigqmcut_md.save with mdout.img_center_bigqmcut_md PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md_hot_start diffing crambin_md_hot_start.out.save with crambin_md_hot_start.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap diffing tip3p_cap.out.save with tip3p_cap.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md diffing tip3p_cap_md.out.save with tip3p_cap_md.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake diffing tip3p_cap_md_shake.out.save with tip3p_cap_md_shake.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake_qmshakeoff diffing tip3p_cap_md_shake_qmshake_off.out.save with tip3p_cap_md_shake_qmshake_off.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_lowmem && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.mg_periodic_vsolv_wat diffing mg_periodic_vsolv_wat.out.save with mg_periodic_vsolv_wat.out PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.1NLN_MD_ntb1_vsolv diffing mdout.1NLN_MD_ntb1_vsolv.save with mdout.1NLN_MD_ntb1_vsolv PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.crambin_md_pm3mmx diffing crambin_md_pm3mmx.out.save with crambin_md_pm3mmx.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.crambin_md_pm3mmx2 diffing crambin_md_pm3mmx2.out.save with crambin_md_pm3mmx2.out PASSED ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/PM3-MAIS && ./Run.zundel diffing zundel.mdout.save with zundel.mdout PASSED ============================================================== diffing zundel.mdcrd.save with zundel.mdcrd PASSED ============================================================== cd qmmm2/PM3-MAIS && ./Run.hcl_wat diffing hcl_wat.mdout.save with hcl_wat.mdout PASSED ============================================================== diffing hcl_wat.mdcrd.save with hcl_wat.mdcrd PASSED ============================================================== cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_PDDGPM3 diffing mdout.MechEm_PDDGPM3.save with mdout.MechEm_PDDGPM3 PASSED ============================================================== cd qmmm2/qmmm_switching_func && ./Run.nma_md_switching diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb0 diffing nma_md_qmgb0.out.save with nma_md_qmgb0.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb1 diffing nma_md_qmgb1.out.save with nma_md_qmgb1.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2 diffing nma_md_qmgb2.out.save with nma_md_qmgb2.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2_saltcon diffing nma_md_qmgb2_saltcon.out.save with nma_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_disp diffing nma_disper.out.save with nma_disper.out PASSED ============================================================== diffing DISP.CHEK.save with DISP.CHEK PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_shake_DFTB && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_dis_neg diffing lysine_md_lnk_dis_neg.out.save with lysine_md_lnk_dis_neg.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_method2 diffing lysine_md_lnk_method2.out.save with lysine_md_lnk_method2.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_qmmm_int0 diffing lysine_md_qmmm_int0.out.save with lysine_md_qmmm_int0.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb2 diffing lysine_md_igb2.out.save with lysine_md_igb2.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb5 diffing lysine_md_igb5.out.save with lysine_md_igb5.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb7 diffing lysine_md_igb7.out.save with lysine_md_igb7.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q1 diffing lysine_md_adjust_q1.out.save with lysine_md_adjust_q1.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q2 diffing lysine_md_adjust_q2.out.save with lysine_md_adjust_q2.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_qmgb2_alpb && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA diffing mdout_PA.save with mdout_PA PASSED ============================================================== cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR diffing mdout_PR.save with mdout_PR PASSED ============================================================== cd qmmm_DFTB/3rd-order/water && ./Run.water diffing mdout.save with mdout PASSED ============================================================== cd qmmm_DFTB/3rd-order/water && ./Run.water_read_mdin diffing mdout.read_mdin.save with mdout.read_mdin PASSED ============================================================== cd qmmm_DFTB/3rd-order/water && ./Run.water_read_file diffing mdout.read_file.save with mdout.read_file PASSED ============================================================== cd qmmm_DFTB/dftb3/water && ./Run.h2o.go diffing h2o.go.out.save with h2o.go.out PASSED ============================================================== cd qmmm_DFTB/dftb3/water && ./Run.h2o.md diffing h2o.md.out.save with h2o.md.out PASSED ============================================================== cd qmmm_DFTB/crambin_DFTB && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md_hot_start diffing crambin_md_hot_start.out.save with crambin_md_hot_start.out PASSED ============================================================== cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_calc_mulliken diffing crambin_md_calc_mulliken.out.save with crambin_md_calc_mulliken.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2 diffing crambin_md_qmgb2.out.save with crambin_md_qmgb2.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_alpb diffing crambin_md_qmgb2_alpb.out.save with crambin_md_qmgb2_alpb.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq1 diffing crambin_md_qmgb2_aq1.out.save with crambin_md_qmgb2_aq1.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq2 diffing crambin_md_qmgb2_aq2.out.save with crambin_md_qmgb2_aq2.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_saltcon diffing crambin_md_qmgb2_saltcon.out.save with crambin_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1 diffing mdout.aladip_ewald_ntb1.save with mdout.aladip_ewald_ntb1 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_link_atoms diffing mdout.aladip_ewald_ntb1_link_atoms.save with mdout.aladip_ewald_ntb1_link_atoms PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_qmewald2 diffing mdout.aladip_ewald_ntb1_qmewald2.save with mdout.aladip_ewald_ntb1_qmewald2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb2 diffing mdout.aladip_ewald_ntb2.save with mdout.aladip_ewald_ntb2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb1 diffing mdout.aladip_pme_ntb1.save with mdout.aladip_pme_ntb1 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2 diffing mdout.aladip_pme_ntb2.save with mdout.aladip_pme_ntb2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms diffing mdout.aladip_pme_ntb2_link_atoms.save with mdout.aladip_pme_ntb2_link_atoms PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq1 diffing mdout.aladip_pme_ntb2_link_atoms_aq1.save with mdout.aladip_pme_ntb2_link_atoms_aq1 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq2 diffing mdout.aladip_pme_ntb2_link_atoms_aq2.save with mdout.aladip_pme_ntb2_link_atoms_aq2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_qmewald2 diffing mdout.aladip_pme_ntb2_qmewald2.save with mdout.aladip_pme_ntb2_qmewald2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_telec diffing mdout.aladip_pme_ntb2_telec.save with mdout.aladip_pme_ntb2_telec PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged diffing mdout.notimaged.save with mdout.notimaged PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md diffing mdout.notimaged_md.save with mdout.notimaged_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme diffing mdout.notimaged_md_pme.save with mdout.notimaged_md_pme PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme_qmewald diffing mdout.notimaged_md_pme_qmewald.save with mdout.notimaged_md_pme_qmewald PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged diffing mdout.imaged.save with mdout.imaged PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged_md diffing mdout.imaged_md.save with mdout.imaged_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center diffing mdout.img_center.save with mdout.img_center PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_md diffing mdout.img_center_md.save with mdout.img_center_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_bigqmcut_md diffing mdout.img_center_bigqmcut_md.save with mdout.img_center_bigqmcut_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut_lowmem && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap diffing tip3p_cap.out.save with tip3p_cap.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md diffing tip3p_cap_md.out.save with tip3p_cap_md.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake diffing tip3p_cap_md_shake.out.save with tip3p_cap_md_shake.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake_qmshakeoff diffing tip3p_cap_md_shake_qmshake_off.out.save with tip3p_cap_md_shake_qmshake_off.out PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_min diffing mdout.1NLN_min.save with mdout.1NLN_min PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1 diffing mdout.1NLN_MD_ntb1.save with mdout.1NLN_MD_ntb1 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_dis_neg diffing mdout.1NLN_MD_ntb1_lnk_dis_neg.save with mdout.1NLN_MD_ntb1_lnk_dis_neg PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_method2 diffing mdout.1NLN_MD_ntb1_lnk_method2.save with mdout.1NLN_MD_ntb1_lnk_method2 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1 diffing mdout.1NLN_MD_ntb1_aq1.save with mdout.1NLN_MD_ntb1_aq1 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1_disp diffing mdout.1NLN_MD_ntb1_aq1_disp.save with mdout.1NLN_MD_ntb1_aq1_disp PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq2 diffing mdout.1NLN_MD_ntb1_aq2.save with mdout.1NLN_MD_ntb1_aq2 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_qmewald2 diffing mdout.1NLN_MD_ntb1_qmewald2.save with mdout.1NLN_MD_ntb1_qmewald2 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb2 diffing mdout.1NLN_MD_ntb2.save with mdout.1NLN_MD_ntb2 PASSED ============================================================== cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA diffing mdout_PA.save with mdout_PA PASSED ============================================================== cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR diffing mdout_PR.save with mdout_PR PASSED ============================================================== cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_DFTB diffing mdout.MechEm_DFTB.save with mdout.MechEm_DFTB PASSED ============================================================== cd qmmm_DFTB/dftb3/nma-h2o-box && ./Run.nma-spcfw-15.md diffing nma-spcfw-15.md.out.save with nma-spcfw-15.md.out PASSED ============================================================== cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF dftb executable is called dftb.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb_md ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF dftb executable is called dftb.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz_md ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.template.lda-sz ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g_md GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.template.bp86_6-31g GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g_md TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.template.blyp_6-31g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g16 or g09 or g03. cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g_md GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g16 or g09 or g03. cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.template.blyp_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g16 or g09 or g03. cd qmmm_EXTERN/pure_QM_MD_Quick && ./Run.h2o.blyp_6-31g Quick not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_Quick && ./Run.h2o.blyp_6-31g_md Quick not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_Quick && ./Run.h2o.hf_sto-3g Quick not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_Quick && ./Run.h2o.template.blyp_6-31g Quick not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g_md Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.template.blyp_6-31g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g_md NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.template.blyp_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.blyp_6-31g_md Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_MRCC && ./Run.h2o.hf_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_MRCC && ./Run.h2o.template.blyp_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_MRCC && ./Run.h2o.blyp_6-31g_md MRCC not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_ADF && ./Run.aladip.blyp_dz.MechEm ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/QMMM_MD_ADF && ./Run.nma-spcfw-15.blyp_dz.MechEm ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g.MechEm Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g.MechEm TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g.MechEm TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.aladip.hf_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g16 or g09 or g03. cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.nma-spcfw-15.hf_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g16 or g09 or g03. cd qmmm_EXTERN/QMMM_MD_Quick && ./Run.aladip.hf_sto-3g Quick not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_Quick && ./Run.aladip.hf_sto-3g.MechEm Quick not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_Quick && ./Run.nma-spcfw-15.hf_sto-3g Quick not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_Quick && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Quick not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_NWChem && ./Run.aladip.hf_sto-3g NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.aladip.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.aladip.hf_sto-3g.MechEm Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.nma-spcfw-15.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_MRCC && ./Run.aladip.hf_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_MRCC && ./Run.nma-spcfw-15.hf_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/QMMM_Lio/water && ./Run.water Lio is not installed - Skipping Test... Check your Lio installation and the LIOHOME environment setting cd qmmm_EXTERN/QMMM_Lio/water && ./Run.td.water Lio is not installed - Skipping Test... Check your Lio installation and the LIOHOME environment setting cd qmmm_EXTERN/QMMM_Fireball/min && ./Run.min Not compiled with Fireball - Skipping Test... cd qmmm_EXTERN/QMMM_Fireball/md && ./Run.md Not compiled with Fireball - Skipping Test... cd abfqmmm/abfqmmm_water_sp && ./Run.abfqmmm_water_sp diffing abfqmmm_water_sp.out.save with abfqmmm_water_sp.out PASSED ============================================================== diffing abfqmmm_water_sp.frc.save with abfqmmm_water_sp.frc PASSED ============================================================== diffing abfqmmm_water_sp.pdb.save with abfqmmm_water_sp.pdb PASSED ============================================================== diffing abfqmmm_water_sp.idrst.save with abfqmmm_water_sp.idrst PASSED ============================================================== cd abfqmmm/abfqmmm_water_md && ./Run.abfqmmm_water_md diffing abfqmmm_water_md.out.save with abfqmmm_water_md.out PASSED ============================================================== diffing abfqmmm_water_md.frc.save with abfqmmm_water_md.frc PASSED ============================================================== diffing abfqmmm_water_md.pdb.save with abfqmmm_water_md.pdb PASSED ============================================================== diffing abfqmmm_water_md.idrst.save with abfqmmm_water_md.idrst PASSED ============================================================== cd abfqmmm/abfqmmm_dmpoh_md && ./Run.abfqmmm_dmpoh_md diffing abfqmmm_dmpoh_md.out.save with abfqmmm_dmpoh_md.out PASSED ============================================================== diffing abfqmmm_dmpoh_md.frc.save with abfqmmm_dmpoh_md.frc PASSED ============================================================== diffing abfqmmm_dmpoh_md.pdb.save with abfqmmm_dmpoh_md.pdb PASSED ============================================================== diffing abfqmmm_dmpoh_md.idrst.save with abfqmmm_dmpoh_md.idrst PASSED ============================================================== diffing abfqmmm_dmpoh_md.rst.save with abfqmmm_dmpoh_md.rst PASSED ============================================================== cd abfqmmm/abfqmmm_lysozyme_md && ./Run.abfqmmm_lysozyme_md diffing abfqmmm_lysozyme_md.out.save with abfqmmm_lysozyme_md.out PASSED ============================================================== diffing abfqmmm_lysozyme_md.frc.save with abfqmmm_lysozyme_md.frc PASSED ============================================================== diffing abfqmmm_lysozyme_md.pdb.save with abfqmmm_lysozyme_md.pdb PASSED ============================================================== diffing abfqmmm_lysozyme_md.idrst.save with abfqmmm_lysozyme_md.idrst PASSED ============================================================== cd abfqmmm/adqmmm_water_md && ./Run.adqmmm_water_md diffing adqmmm_water_md.out.save with adqmmm_water_md.out PASSED ============================================================== diffing adqmmm_water_md.frc.save with adqmmm_water_md.frc PASSED ============================================================== diffing adqmmm_water_md.pdb.save with adqmmm_water_md.pdb PASSED ============================================================== diffing adqmmm_water_md.idrst.save with adqmmm_water_md.idrst PASSED ============================================================== cd abfqmmm/hotspot_water_md && ./Run.hotspot_water_md diffing hotspot_water_md.out.save with hotspot_water_md.out PASSED ============================================================== diffing hotspot_water_md.frc.save with hotspot_water_md.frc PASSED ============================================================== diffing hotspot_water_md.pdb.save with hotspot_water_md.pdb PASSED ============================================================== diffing hotspot_water_md.idrst.save with hotspot_water_md.idrst PASSED ============================================================== cd sebomd/AM1/dimethylether && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1/methionine && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1/nucleoside && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1/water1 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-PhoT/dimethylether && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-PhoT/methionine && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-PhoT/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-PhoT/nucleoside && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-PhoT/water1 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-CB1/dimethylether && ./min.csh && ./md.csh diffing min.out.save with min.out possible FAILURE: (ignored) check min.out.dif ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-CB1/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/AM1-d-CB1/water1 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/DC/water32 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/Ewald-CM1/Water2 && ./md.csh diffing md.out.save with md.out PASSED ============================================================== cd sebomd/Ewald-ConstantCharge/Water2 && ./md.csh diffing md.out.save with md.out PASSED ============================================================== cd sebomd/Ewald-Mulliken/Water2 && ./md.csh diffing md.out.save with md.out PASSED ============================================================== cd sebomd/MinimumImage/Water2 && ./md.csh diffing md.out.save with md.out PASSED ============================================================== cd sebomd/method3/alaninedipeptide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/method3/ethanol_and_water && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/MNDO/dimethylether && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/MNDO/methionine && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/MNDO/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/MNDO/nucleoside && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/MNDO/water1 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/RM1/dimethylether && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/RM1/methionine && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/RM1/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/RM1/nucleoside && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== # -cd sebomd/RM1/water1 && ./min.csh && ./md.csh cd sebomd/RM1/water1 && ./md.csh diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PIF2/dimethylether && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PIF2/water1 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PIF2/doublewater && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PIF2/ethanol_and_water && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PIF3/water1 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PIF3/doublewater && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PIF3/ethanol_and_water && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PM3/alaninedipeptide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PM3/dimethylether && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PM3/methionine && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PM3/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PM3/nucleoside && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== cd sebomd/PM3/water1 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== export TESTsander='/usr/local/amber22///bin/sander'; unset DO_PARALLEL; cd emil/emil_sander_gbsa && ./Run.emil EMIL DO_PARALLEL not set... testing emil in serial. diffing mdout.emil.0.0.save with mdout.emil.0.0 PASSED ============================================================== diffing emil.log.0.0.save with emil.log.0.0 PASSED ============================================================== diffing mdout.emil.0.1.save with mdout.emil.0.1 PASSED ============================================================== diffing emil.log.0.1.save with emil.log.0.1 PASSED ============================================================== diffing mdout.emil.0.9.save with mdout.emil.0.9 PASSED ============================================================== diffing emil.log.0.9.save with emil.log.0.9 PASSED ============================================================== cd sanderapi && make test make[3]: Entering directory '/usr/local/amber22/test/sanderapi' (if [ -f "/usr/local/amber22///lib/libsander.so" ]; then \ make test_all; \ else \ make test_none; \ fi;) make[4]: Entering directory '/usr/local/amber22/test/sanderapi' Creating the bad prmtop test.parm7 Testing the Fortran API /usr/bin/gfortran -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -I/usr/local/amber22///include -L/usr/local/amber22///lib test.F90 -o testf -lsander Running testf Testing proper treatment of a bad prmtop; an error message is expected: ERROR: Flag "ATOM_NAME" not found in PARM file PASSED ============================================================== Testing proper treatment of bad input: unreasonably small cut for non-periodic run: 1.00 PASSED ============================================================== Testing GB sander interface PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the QM/MM non-periodic interface PASSED ============================================================== Testing the QM/MM periodic interface (PM3-PDDG) PASSED ============================================================== Testing the QM/MM periodic interface (DFTB) PASSED ============================================================== Testing the broader API functionality PASSED ============================================================== Checking get_positions call PASSED ============================================================== Testing the Fortran file-less API /usr/bin/gfortran -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -I/usr/local/amber22///include -L/usr/local/amber22///lib test2.F90 -o testf2 -lsander Running testf2 Testing GB sander interface PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the QM/MM non-periodic interface PASSED ============================================================== Testing the QM/MM periodic interface (PM3-PDDG) PASSED ============================================================== Testing the C API /usr/bin/gcc -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -I/usr/local/amber22///include -L/usr/local/amber22///lib test.c -o testc -lsander test.c: In function ‘main’: test.c:163:5: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation] 163 | strncpy(qmmm_options.qm_theory, "PM3", 3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.c:207:5: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 207 | strncpy(qmmm_options.qmmask, ":1-2", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.c:208:5: warning: ‘strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] 208 | strncpy(qmmm_options.qm_theory, "PDDG-PM3", 8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.c:248:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 248 | strncpy(qmmm_options.qmmask, ":1-2", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.c:249:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 249 | strncpy(qmmm_options.qm_theory, "DFTB", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Running testc Testing proper treatment of a bad prmtop; an error message is expected: ERROR: Flag "ATOM_NAME" not found in PARM file PASSED ============================================================== Testing proper treatment of bad input: unreasonably small cut for non-periodic run: 5.00 PASSED ============================================================== Testing GB sander interface PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the QM/MM non-periodic interface PASSED ============================================================== Testing the QM/MM periodic interface (PM3-PDDG) PASSED ============================================================== Testing the QM/MM periodic interface (DFTB) PASSED ============================================================== Testing the broader API functionality PASSED ============================================================== Checking get_positions call PASSED ============================================================== Testing the C++ API /usr/bin/g++ -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -I/usr/local/amber22///include -L/usr/local/amber22///lib test.cpp -o testcpp -lsander test.cpp: In function ‘int main()’: test.cpp:162:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation] 162 | strncpy(qmmm_options.qm_theory, "PM3", 3); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.cpp:206:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 206 | strncpy(qmmm_options.qmmask, ":1-2", 4); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.cpp:207:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] 207 | strncpy(qmmm_options.qm_theory, "PDDG-PM3", 8); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.cpp:247:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 247 | strncpy(qmmm_options.qmmask, ":1-2", 4); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test.cpp:248:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 248 | strncpy(qmmm_options.qm_theory, "DFTB", 4); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Running testcpp Testing GB sander interface PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Checking for consistent forces PASSED ============================================================== Testing the QM/MM non-periodic interface PASSED ============================================================== Testing the QM/MM periodic interface (PM3-PDDG) PASSED ============================================================== Testing the QM/MM periodic interface (DFTB) PASSED ============================================================== Testing the broader API functionality PASSED ============================================================== Checking get_positions call PASSED ============================================================== Testing the Python API /usr/local/amber22//miniconda/bin/python test.py Testing GB sander interface PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Checking for consistent forces PASSED ============================================================== Testing the QM/MM non-periodic interface PASSED ============================================================== Testing the QM/MM periodic interface (PM3-PDDG) PASSED ============================================================== Testing the QM/MM periodic interface (DFTB) Could not find the SLKO files. Skipping this test. ============================================================== Testing the broader API functionality PASSED ============================================================== Checking get_positions call PASSED ============================================================== Checking context manager functionality PASSED ============================================================== Testing belly = True PASSED ============================================================== Testing belly = False PASSED ============================================================== Testing restraintmask PASSED ============================================================== /bin/rm -f test.parm7 testf testf2 testc testcpp make[4]: Leaving directory '/usr/local/amber22/test/sanderapi' make[3]: Leaving directory '/usr/local/amber22/test/sanderapi' cd sanderlesapi && make test make[3]: Entering directory '/usr/local/amber22/test/sanderlesapi' (if [ -f "/usr/local/amber22///lib/libsanderles.so" ]; then \ make test_all; \ else \ make test_none; \ fi;) make[4]: Entering directory '/usr/local/amber22/test/sanderlesapi' Testing the Fortran LES API /usr/bin/gfortran -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -fallow-argument-mismatch -fno-inline-arg-packing -I/usr/local/amber22///include -L/usr/local/amber22///lib test.F90 -o testf -lsanderles Running testf Testing GB sander interface (diffcoords w/ RDT) PASSED ============================================================== Testing GB sander interface (samecoords w/out RDT) PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the C LES API /usr/bin/gcc -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -I/usr/local/amber22///include -L/usr/local/amber22///lib test.c -o testc -lsanderles Running testc Testing GB sander interface (diffcoords w/ RDT) PASSED ============================================================== Testing GB sander interface (samecoords w/out RDT) PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the C++ LES API /usr/bin/g++ -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -I/usr/local/amber22///include -L/usr/local/amber22///lib test.cpp -o testcpp -lsanderles Running testcpp Testing GB sander interface (diffcoords w/ RDT) PASSED ============================================================== Testing GB sander interface (samecoords w/out RDT) PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the Python LES API /usr/local/amber22//miniconda/bin/python test.py Testing GB sander interface (diffcoords w/ RDT) PASSED ============================================================== Testing GB sander interface (samecoords w/out RDT) PASSED ============================================================== Testing PME sander interface PASSED ============================================================== make[4]: Leaving directory '/usr/local/amber22/test/sanderlesapi' make[3]: Leaving directory '/usr/local/amber22/test/sanderlesapi' make[2]: Leaving directory '/usr/local/amber22/test' make[2]: Entering directory '/usr/local/amber22/test' cd 2048_wat_gem && ./Run.2048_wat_nvt_gem.pmemd.gemstar diffing mdout.2048_wat_nvt_gem.pmemd.gemstar.save with mdout.2048_wat_nvt_gem.pmemd.gemstar PASSED ============================================================== cd 2048_wat_gem && ./Run.2048_wat_MCbar_gem.pmemd.gemstar diffing mdout.2048_wat_MCbar_gem.pmemd.gemstar.save with mdout.2048_wat_MCbar_gem.pmemd.gemstar PASSED ============================================================== cd 2048_wat_gem && ./Run.2048_wat_nvt_gem.pmemd.gem Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.2048_wat_nvt_gem.pmemd.gem.save with mdout.2048_wat_nvt_gem.pmemd.gem PASSED ============================================================== cd 2048_wat_gem && ./Run.2048_wat_MCbar_gem.pmemd.gem Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.2048_wat_MCbar_gem.pmemd.gem.save with mdout.2048_wat_MCbar_gem.pmemd.gem PASSED ============================================================== cd amoeba_formbox && ./Run.amoeba_formbox.pmemd.gem diffing amoeba_formbox.pmemd.gem.mdout.save with amoeba_formbox.pmemd.gem.mdout PASSED ============================================================== cd amoeba_IL && ./Run.amoeba_IL.pmemd.gem diffing mdout.amoeba_IL.pmemd.gem.save with mdout.amoeba_IL.pmemd.gem PASSED ============================================================== cd amoeba_jac3 && ./Run.jac_amba_beeman_MCbar.pmemd.gem diffing mdout.jac_amba_beeman_MCbar.pmemd.gem.save with mdout.jac_amba_beeman_MCbar.pmemd.gem PASSED ============================================================== cd amoeba_jac3 && ./Run.jac_amba_beeman_nvt.pmemd.gem diffing mdout.jac_amba_beeman_nvt.pmemd.gem.save with mdout.jac_amba_beeman_nvt.pmemd.gem PASSED ============================================================== cd amoeba_jac3 && ./Run.jac_amba_beeman_virial.pmemd.gem diffing mdout.jac_amba_beeman_virial.pmemd.gem.save with mdout.jac_amba_beeman_virial.pmemd.gem PASSED ============================================================== cd amoeba_jac3 && ./Run.jac_amba_verlet_nvt.pmemd.gem diffing mdout.jac_amba_verlet_nvt.pmemd.gem.save with mdout.jac_amba_verlet_nvt.pmemd.gem PASSED ============================================================== cd amoeba_gb1 && ./Run.amoeba_gb1.pmemd.gem diffing mdout.amoeba_gb1.pmemd.gem.save with mdout.amoeba_gb1.pmemd.gem PASSED ============================================================== cd amoeba_wat1 && ./Run.amoeba_wat1.pmemd.gem diffing amoeba_wat1.pmemd.gem.out.save with amoeba_wat1.pmemd.gem.out PASSED ============================================================== cd amoeba_wat2 && ./Run.amoeba_wat2.ntpverlet.pmemd.gem diffing amoeba_wat2.ntpverlet.pmemd.gem.out.save with amoeba_wat2.ntpverlet.pmemd.gem.out PASSED ============================================================== cd amoeba_wat2 && ./Run.amoeba_wat2.pmemd.gem diffing amoeba_wat2.pmemd.gem.out.save with amoeba_wat2.pmemd.gem.out PASSED ============================================================== make[2]: Leaving directory '/usr/local/amber22/test' make[2]: Entering directory '/usr/local/amber22/AmberTools/test' Finished serial test suite for AmberTools at Saturday 22 October 2022 01:38:54 PM IST. make[2]: Leaving directory '/usr/local/amber22/AmberTools/test' 2685 file comparisons passed 4 file comparisons failed (2 of which can be ignored) 0 tests experienced errors Test log file saved as /usr/local/amber22///logs/test_at_serial/2022-10-22_11-50-17.log Test diffs file saved as /usr/local/amber22///logs/test_at_serial/2022-10-22_11-50-17.diff