(find . -name '*.dif' -o -name 'profile_mpi' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) rm -f TEST_FAILURES.diff 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 possible FAILURE: check mdout.tip5p.dif ============================================================== 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 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 possible FAILURE: check gcg.dip.o.dif ============================================================== 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 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 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 executing: java -jar ./Run.jar Invalid or corrupt jarfile ./Run.jar The execution of ./Run.jar failed. The reason is probably that ./Run.jar doesn't contain the MainClass in MANIFEST.MF. If you want to unpack ./Run.jar, call: jar -xf ./Run.jar 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 bintraj && ./Run.bintraj ../../src/netcdf/bin/ncdump: Command not found. diffing nc_headers.save with nc_headers possible FAILURE: check nc_headers.dif ============================================================== 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 10 SANDER.LES test, no PME diffing md.LES.out.save with md.LES.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_cmd_water/equilib && ./Run.cmdyn diffing h2o_les.top.save with h2o_les.top PASSED ============================================================== diffing h2o_les.crd.save with h2o_les.crd PASSED ============================================================== diffing cmd.out.save with cmd.out PASSED ============================================================== cd PIMD/part_cmd_water/start && ./Run.cmdyn diffing cmd.out.save with cmd.out PASSED ============================================================== cd PIMD/part_cmd_water/restart && ./Run.cmdyn diffing cmd.out.save with cmd.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 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 PASSED ============================================================== cd amoeba_formbox && ./Run.amoeba_formbox diffing amoeba_formbox.mdout.save with amoeba_formbox.mdout PASSED ============================================================== cd ncsu && ./run-serial.sh >>>>>>> doing 'abmd_ANALYSIS' >>>>>>> doing 'abmd_FLOODING' >>>>>>> doing 'abmd_UMBRELLA' >>>>>>> doing 'smd' diffing save/mdout with mdout PASSED ============================================================== diffing save/smd.txt with smd.txt PASSED ============================================================== >>>>>>> doing 'pmd' diffing save/mdout with mdout PASSED ============================================================== diffing save/pmd.txt with pmd.txt 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 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 pbsa_decres && ./Run.pbsa_decres diffing mdout.pbsa_decres.save with mdout.pbsa_decres PASSED ============================================================== cd pbsa_decpw && ./Run.pbsa_decpw diffing mdout.pbsa_decpw.save with mdout.pbsa_decpw PASSED ============================================================== cd ambpdb && ./Run.ambpdb | New format PARM file being parsed. | Version = 1.000 Date = 02/19/04 Time = 15:33:29 diffing restrt.pdb.save with restrt.pdb PASSED ============================================================== cd ambpdb_first_protein && ./Run.ambpdb | New format PARM file being parsed. | Version = 1.000 Date = 02/15/07 Time = 16:57:28 diffing first.pdb.save with first.pdb possible FAILURE: check first.pdb.dif ============================================================== cd ambpdb_first_rna && ./Run.ambpdb | New format PARM file being parsed. | Version = 1.000 Date = 05/18/06 Time = 18:52:52 diffing first.pdb.save with first.pdb possible FAILURE: check first.pdb.dif ============================================================== cd elsize && ./Run.elsize diffing elsize_out.trxox.save with elsize_out.trxox PASSED ============================================================== Finished serial test suite for the MM portions of Amber 10; to test QM/MM, type 'make test.serial.QMMM'