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 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.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_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_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 dhfr; ./Run.dhfr diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== cd dhfr; ./Run.dhfr.noshake diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake PASSED ============================================================== cd dhfr; ./Run.dhfr.min diffing mdout.dhfr.min.save with mdout.dhfr.min 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_sgld diffing mdout.ips_sgld.save with mdout.ips_sgld 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 rstdip.save with rstdip PASSED ============================================================== diffing restrt.save with restrt 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 tgtmd/change_target; ./Run.tgtmd SANDER: Targeted MD with changing target diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.rms; ./Run.tgtmd SANDER: Targeted MD with changing target and fit/rmsd to different regions diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.ntr; ./Run.tgtmd SANDER: Targeted MD with changing target and restraints diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/conserve_ene; ./Run.tgtmd SANDER: Targeted MD energy conservation test diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/minimize; ./Run.tgtmin SANDER: Targeted minimization diffing tgtmin.out.save with tgtmin.out PASSED ============================================================== cd tgtmd/PME; ./Run.tgtPME SANDER: Targeted MD with PME diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd trajene; ./Run.trajene diffing trajene.out.save with trajene.out PASSED ============================================================== cd alp; ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== cd pb_pgb; ./Run.pbpgb diffing mdout.pbpgb.save with mdout.pbpgb 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.jar diffing mdout.jar.save with mdout.jar possible FAILURE: check mdout.jar.dif ============================================================== diffing dist_vs_t.save with dist_vs_t PASSED ============================================================== cd bintraj; ./Run.bintraj sander and ptraj: test sander netCDF output and ptraj netCDF input diffing nc_headers.save with nc_headers PASSED ============================================================== diffing rms.save with rms 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 gb_rna; ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== cd gbsa_xfin; ./Run.gbsa diffing mdout.gbsa.save with mdout.gbsa 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 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 alpb_trx; ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd cnstph; ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== cd gb1_cox2; ./Run.cox2 diffing cox2.out.save with cox2.out 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 Amber 8 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 Amber 8 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 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_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_doublet diffing nma_md_doublet.out.save with nma_md_doublet.out PASSED ============================================================== cd qmmm2/pure_QM_MD; ./Run.nma_md_triplet diffing nma_md_triplet.out.save with nma_md_triplet.out PASSED ============================================================== cd qmmm2/pure_QM_MD; ./Run.nma_md_quartet diffing nma_md_quartet.out.save with nma_md_quartet.out PASSED ============================================================== cd qmmm2/pure_QM_MD; ./Run.nma_md_quintet diffing nma_md_quintet.out.save with nma_md_quintet.out PASSED ============================================================== cd qmmm2/pure_QM_MD; ./Run.nma_md_sextet diffing nma_md_sextet.out.save with nma_md_sextet.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_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_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 qmmm2/1-2-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_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_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_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_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/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_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/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 ============================================================== echo "skipping the DFTB tests because needed parameters files are missing" skipping the DFTB tests because needed parameters files are missing echo "skipping the DFTB tests because needed parameters files are missing" skipping the DFTB tests because needed parameters files are missing cd pimd_water/P=8/pimd; ./Run.pimd diffing md.out.save with md.out PASSED ============================================================== cd pimd_water/P=16/pimd; ./Run.pimd diffing md.out.save with md.out PASSED ============================================================== cd pimd_water/P=32/pimd; ./Run.pimd diffing md.out.save with md.out PASSED ============================================================== cd neb_gb; ./Run.neb.sa diffing mdout.neb.save with mdout.neb PASSED ============================================================== cd qmmm2/neb_gb; ./Run.neb_link_atoms diffing neb_qm_link.out.save with neb_qm_link.out possible FAILURE: check neb_qm_link.out.dif ============================================================== cd qmmm2/neb_gb; ./Run.neb_link_atoms_qmgb2 diffing neb_qm_link_qmgb2.out.save with neb_qm_link_qmgb2.out PASSED ============================================================== cd qmmm2/neb_gb; ./Run.neb_qmgb2 diffing neb_pure_qm_qmgb2.out.save with neb_pure_qm_qmgb2.out PASSED ============================================================== cd qmmm2/neb_gb; ./Run.neb diffing neb_pure_qm.out.save with neb_pure_qm.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd pimd_helium/P=4/pimd; ./Run.pimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd 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 ============================================================== diffing spcfw_nscm.out.save with spcfw_nscm.out PASSED ============================================================== cd pimd_gb/; ./Run.pimd diffing pimd_gb1.out.save with pimd_gb1.out PASSED ============================================================== diffing pimd_gb2.out.save with pimd_gb2.out PASSED ============================================================== diffing pimd_gb5.out.save with pimd_gb5.out PASSED ============================================================== diffing pimd_gb6.out.save with pimd_gb6.out PASSED ============================================================== diffing pimd_gb7.out.save with pimd_gb7.out PASSED ============================================================== diffing pimd_gb1_nscm.out.save with pimd_gb1_nscm.out PASSED ============================================================== cd qmmm2/pimd_gb; ./Run.pimd diffing pimd_qmgb2_igb1.out.save with pimd_qmgb2_igb1.out PASSED ============================================================== cd qmmm2/pimd_pme; ./Run.pimd diffing pimd_qmewald1.out.save with pimd_qmewald1.out PASSED ============================================================== diffing pimd_qmewald2.out.save with pimd_qmewald2.out PASSED ============================================================== cd water2_qmmmnmr; ./Run.wnmr diffing mdout.wnmr.save with mdout.wnmr PASSED ============================================================== diffing divcon.out.save with divcon.out PASSED ============================================================== cd crambin_qmmmnmr; ./Run.cnmr diffing mdout.cnmr.save with mdout.cnmr PASSED ============================================================== diffing divcon.out.save with divcon.out PASSED ============================================================== cd qmmm2/crambin; ./Run.crambin_divcon diffing crambin_divcon.out.save with crambin_divcon.out possible FAILURE: check crambin_divcon.out.dif ============================================================== cd qmmm2/lysine_PM3; ./Run.lysine_divcon diffing lysine_divcon.out.save with lysine_divcon.out PASSED ============================================================== cd qmmm2/lysine_PM3; ./Run.lysine_md_divcon diffing lysine_md_divcon.out.save with lysine_md_divcon.out PASSED ============================================================== cd qmmm2/lysine_AM1; ./Run.lysine_divcon diffing lysine_divcon.out.save with lysine_divcon.out PASSED ============================================================== cd qmmm2/2pk4; ./Run.2pk4_stan diffing 2pk4_stan.out.save with 2pk4_stan.out PASSED ============================================================== cd amoeba_wat1; ./Run.amoeba_wat1 diffing amoeba_wat1.out.save with amoeba_wat1.out PASSED ============================================================== cd amoeba_wat2; ./Run.amoeba_wat2 diffing amoeba_wat2.out.save with amoeba_wat2.out PASSED ============================================================== cd amoeba_wat2; ./Run.ntpverlet diffing ntpverlet.save with ntpverlet PASSED ============================================================== cd amoeba_gb1; ./Run.amoeba_gb1 diffing mdout.amoeba_gb1.save with mdout.amoeba_gb1 PASSED ============================================================== cd amoeba_jac; ./Run.amoeba_jac diffing amoeba_jac.mdout.save with amoeba_jac.mdout possible FAILURE: check amoeba_jac.mdout.dif ============================================================== cd amoeba_formbox; ./Run.amoeba_formbox diffing amoeba_formbox.mdout.save with amoeba_formbox.mdout 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 vac_rna; ./Run.anal diffing analout.save with analout PASSED ============================================================== cd vac_rna; ./Run.anal_pdb diffing pdb1.save with pdb1 PASSED ============================================================== cd ptraj_matrix; ./Run.matrix ptraj: analyze fluctuation matrices diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat PASSED ============================================================== diffing 1rrb_vac_mwcovarmat_evecs.dat.save with 1rrb_vac_mwcovarmat_evecs.dat PASSED ============================================================== diffing 1rrb_vac_distcovarmat_evecs.dat.save with 1rrb_vac_distcovarmat_evecs.dat PASSED ============================================================== cd ptraj_rms; ./Run.rms ptraj: test rms and 2drms commands diffing rms_fit.dat.save with rms_fit.dat PASSED ============================================================== diffing rms_nofit.dat.save with rms_nofit.dat PASSED ============================================================== diffing rms2d.ps.save with rms2d.ps PASSED ============================================================== cd ptraj_les; ./Run.les ptraj: test ptraj on computing rdf for les file diffing rdf_standard.xmgr.save with rdf_standard.xmgr PASSED ============================================================== diffing rdf_volume.xmgr.save with rdf_volume.xmgr PASSED ============================================================== ptraj: test ptraj on splitting les trajectory to normal trajectory diffing hef_splitted.crd.save with hef_splitted.crd PASSED ============================================================== diffing input.pdb.1.save with input.pdb.1 PASSED ============================================================== diffing input.pdb.2.save with input.pdb.2 PASSED ============================================================== diffing input.pdb.3.save with input.pdb.3 PASSED ============================================================== diffing input.pdb.4.save with input.pdb.4 PASSED ============================================================== diffing input.rst.1.save with input.rst.1 PASSED ============================================================== diffing input.rst.2.save with input.rst.2 PASSED ============================================================== diffing input.rst.3.save with input.rst.3 PASSED ============================================================== diffing input.rst.4.save with input.rst.4 PASSED ============================================================== ptraj: test ptraj on averaging les trajectory to normal trajectory diffing hef_averaged.crd.save with hef_averaged.crd PASSED ============================================================== cd leap; ./Run.tleap Running leap tests on ./tleap -> ../../exe/teLeap building force field libraries: '91 ff.. diffing ../../dat/leap/lib/all_amino91.lib with all_amino91.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminont91.lib with all_aminont91.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib PASSED ============================================================== diffing ../../dat/leap/lib/ions91.lib with ions91.lib PASSED ============================================================== '94 ff.. diffing ../../dat/leap/lib/all_amino94.lib with all_amino94.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_aminont94.lib with all_aminont94.lib PASSED ============================================================== diffing ../../dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib PASSED ============================================================== diffing ../../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 ============================================================== comparing sander energies diffing ff94/sander_mdout.aminoan94.save with ff94/sander_mdout.aminoan94 PASSED ============================================================== - aminonc94 comparing topology to earlier leap version.. diffing ff94/all_aminonc94.top with all_aminonc94.top PASSED ============================================================== comparing sander energies diffing ff94/sander_mdout.aminonc94.save with ff94/sander_mdout.aminonc94 PASSED ============================================================== - dna94 comparing topology to earlier leap version.. diffing ff94/all_dna94.top with all_dna94.top PASSED ============================================================== comparing sander energies diffing ff94/sander_mdout.dna94.save with ff94/sander_mdout.dna94 PASSED ============================================================== - rna94 comparing topology to earlier leap version.. diffing ff94/all_rna94.top with all_rna94.top PASSED ============================================================== comparing sander energies diffing ff94/sander_mdout.rna94.save with ff94/sander_mdout.rna94 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 -------------------------------------------------------------- cd resp; ./Run.ade RESP stage 1: Amber 9 RESP 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: Amber 9 RESP 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 antechamber/tp; ./Run.tp ATTENTION The Mulliken charges were generated by divcon in amber9, you may get different result if different QM program is applied diffing tp.mol2.save with tp.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/ash; ./Run.ash diffing ash.mol2.save with ash.mol2 possible FAILURE: check ash.mol2.dif ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/sustiva; ./Run.sustiva ATTENTION The Mulliken charges were generated by divcon in amber9; you may get different results if a different QM program is applied diffing sustiva.mol2.save with sustiva.mol2 possible FAILURE: check sustiva.mol2.dif ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/fluorescein; ./Run.fluorescein Info: Bond types are assigned for valence state 1 with penalty of 1 diffing fluorescein.mol2.save with fluorescein.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/guanine_amber; ./Run.guanine_amber diffing DGN.mol2.save with DGN.mol2 possible FAILURE: check DGN.mol2.dif ============================================================== cd antechamber/fpph; ./Run.fpph_resp diffing fpph_resp.mol2.save with fpph_resp.mol2 PASSED ============================================================== cd antechamber/top2mol2; ./Run.top2mol2 ---DNA --- ../../../exe/top2mol2 -p dna.prmtop -c dna.prmcrd -o dna.mol2 ../../../exe/top2mol2 -p dna.prmtop -c dna.prmcrd -o dna_wat.mol2 -wt 1 --Amino acid--- ../../../exe/top2mol2 -p aa.prmtop -c aa.prmcrd -o aa.mol2 --Sustiva--- ../../../exe/top2mol2 -p sustiva.prmtop -c sustiva.prmcrd -o sustiva.mol2 diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing dna.mol2.save with dna.mol2 PASSED ============================================================== diffing dna_wat.mol2.save with dna_wat.mol2 PASSED ============================================================== diffing aa.mol2.save with aa.mol2 PASSED ============================================================== cd antechamber/database; ./Run.database diffing total.frcmod.save with total.frcmod PASSED ============================================================== diffing total.prepi.save with total.prepi PASSED ============================================================== cd pbsa_trx; ./Run.trxox.min diffing mdout.trxox.min.save with mdout.trxox.min PASSED ============================================================== cd pbsa_dmp; ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== cd pbsa_pgb; ./Run.pbpgb.min diffing mdout.pbpgb.min.save with mdout.pbpgb.min PASSED ============================================================== cd pbsa_radi; ./Run.ion.min diffing ./out.save/Li.out.save with Li.out PASSED ============================================================== diffing ./out.save/Na.out.save with Na.out PASSED ============================================================== diffing ./out.save/K.out.save with K.out PASSED ============================================================== diffing ./out.save/Rb.out.save with Rb.out PASSED ============================================================== diffing ./out.save/Cs.out.save with Cs.out PASSED ============================================================== diffing ./out.save/F.out.save with F.out PASSED ============================================================== diffing ./out.save/Cl.out.save with Cl.out PASSED ============================================================== diffing ./out.save/IM.out.save with IM.out PASSED ============================================================== diffing ./out.save/Br.out.save with Br.out PASSED ============================================================== diffing ./out.save/I.out.save with I.out PASSED ============================================================== diffing ./out.save/MG.out.save with MG.out PASSED ============================================================== diffing ./out.save/Ca.out.save with Ca.out PASSED ============================================================== diffing ./out.save/Zn.out.save with Zn.out PASSED ============================================================== diffing ./out.save/tp3.out.save with tp3.out PASSED ============================================================== diffing ./out.save/ile.out.save with ile.out PASSED ============================================================== diffing ./out.save/leu.out.save with leu.out PASSED ============================================================== diffing ./out.save/val.out.save with val.out PASSED ============================================================== diffing ./out.save/phe.out.save with phe.out PASSED ============================================================== diffing ./out.save/trp.out.save with trp.out PASSED ============================================================== diffing ./out.save/hid.out.save with hid.out PASSED ============================================================== diffing ./out.save/hie.out.save with hie.out PASSED ============================================================== diffing ./out.save/nhe.out.save with nhe.out PASSED ============================================================== diffing ./out.save/tyr.out.save with tyr.out PASSED ============================================================== diffing ./out.save/ser.out.save with ser.out PASSED ============================================================== diffing ./out.save/thr.out.save with thr.out PASSED ============================================================== diffing ./out.save/cys.out.save with cys.out PASSED ============================================================== diffing ./out.save/cyx.out.save with cyx.out PASSED ============================================================== diffing ./out.save/met.out.save with met.out PASSED ============================================================== diffing ./out.save/lyn.out.save with lyn.out PASSED ============================================================== diffing ./out.save/ash.out.save with ash.out PASSED ============================================================== diffing ./out.save/glh.out.save with glh.out PASSED ============================================================== diffing ./out.save/asn.out.save with asn.out PASSED ============================================================== diffing ./out.save/gln.out.save with gln.out PASSED ============================================================== diffing ./out.save/nma.out.save with nma.out PASSED ============================================================== diffing ./out.save/alabk.out.save with alabk.out PASSED ============================================================== diffing ./out.save/glybk.out.save with glybk.out PASSED ============================================================== diffing ./out.save/probk.out.save with probk.out PASSED ============================================================== diffing ./out.save/da.out.save with da.out PASSED ============================================================== diffing ./out.save/dc.out.save with dc.out PASSED ============================================================== diffing ./out.save/dg.out.save with dg.out PASSED ============================================================== diffing ./out.save/dt.out.save with dt.out PASSED ============================================================== diffing ./out.save/ru.out.save with ru.out PASSED ============================================================== diffing ./out.save/arg.out.save with arg.out PASSED ============================================================== diffing ./out.save/asp.out.save with asp.out PASSED ============================================================== diffing ./out.save/cym.out.save with cym.out PASSED ============================================================== diffing ./out.save/glu.out.save with glu.out PASSED ============================================================== diffing ./out.save/hip.out.save with hip.out PASSED ============================================================== diffing ./out.save/lys.out.save with lys.out PASSED ============================================================== diffing ./out.save/dap.out.save with dap.out PASSED ============================================================== diffing ./out.save/da3p.out.save with da3p.out PASSED ============================================================== diffing ./out.save/da5p.out.save with da5p.out PASSED ============================================================== diffing ./out.save/danp.out.save with danp.out PASSED ============================================================== diffing ./out.save/rap.out.save with rap.out PASSED ============================================================== diffing ./out.save/ra3p.out.save with ra3p.out PASSED ============================================================== diffing ./out.save/ra5p.out.save with ra5p.out PASSED ============================================================== diffing ./out.save/ranp.out.save with ranp.out PASSED ============================================================== cd pbsa_tsr; ./Run.tsrb.min diffing mdout.tsrb.min.save with mdout.tsrb.min PASSED ============================================================== cd ambpdb; ./Run.ambpdb diffing restrt.pdb.save with restrt.pdb PASSED ============================================================== cd elsize; ./Run.elsize diffing elsize_out.trxox.save with elsize_out.trxox PASSED ==============================================================