make[2]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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 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 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.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.lmodxmin diffing mdout.dhfr.lmodxmin.save with mdout.dhfr.lmodxmin 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_sgld diffing mdout.ips_sgld.save with mdout.ips_sgld PASSED ============================================================== cd gact_ips && ./Run.ips_sgldfp diffing mdout.ips_sgldfp.save with mdout.ips_sgldfp 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 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 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 ============================================================== 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 /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/include/netcdf.mod 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.save with mdout.iw2 PASSED ============================================================== diffing mdcrd.save with mdcrd.iw2 PASSED ============================================================== diffing rstrt.save with rstrt.iw2 PASSED ============================================================== /bin/rm: No match. 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 diffing nc_headers.save with nc_headers PASSED ============================================================== cd nc_restart && make -k test make[3]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/test/nc_restart' 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 md.out.save with md.out PASSED ============================================================== Netcdf MD restart read test, ntx=5 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== Netcdf MD restart read test, ntx=1 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== make[3]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/test/nc_restart' 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 amd && ./Run.dhfr.amd3 diffing mdout.dhfr.amd3.save with mdout.dhfr.amd3 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 gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp 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 && ./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 alpb_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox 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_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_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 ============================================================== >>>>>>> doing 'smd2' diffing save/mdout with mdout PASSED ============================================================== diffing save/work.txt with work.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 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/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 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 PASSED dbf_0.dadt checking dadt force PASSED dbf_0.dgdc checking dgdc force PASSED dbf_0.lysasp checking lysasp force PASSED dbf_0.polyALA checking polyALA force PASSED dbf_0.polyAT checking polyAT force PASSED dbf_1.argasp checking argasp force PASSED dbf_1.dadt checking dadt force PASSED dbf_1.dgdc checking dgdc force PASSED dbf_1.lysasp checking lysasp force PASSED dbf_1.polyALA checking polyALA force PASSED dbf_1.polyAT checking polyAT force PASSED dbf_2.argasp checking argasp force PASSED dbf_2.dadt checking dadt force PASSED dbf_2.dgdc checking dgdc force PASSED dbf_2.lysasp checking lysasp force PASSED dbf_2.polyALA checking polyALA force PASSED dbf_2.polyAT checking polyAT force 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 possible FAILURE: check mdout.lig.min.dif ============================================================== 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 ============================================================== if [ -n "" ]; then cd rism3d/ala && ./Run.ala; fi if [ -n "" ]; then cd rism3d/ala && ./Run.ala.mdiis0; fi if [ -n "" ]; then cd rism3d/ala && ./Run.ala.mdiis1; fi if [ -n "" ]; then cd rism3d/ala && ./Run.ala.resize; fi if [ -n "" ]; then cd rism3d/ala && ./Run.ala.dist; fi if [ -n "" ]; then cd rism3d/ala && ./Run.ala.dist.xyzv; fi if [ -n "" ]; then cd rism3d/ala && ./Run.ala.hnc; fi if [ -n "" ]; then cd rism3d/ala && ./Run.ala.pse1; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph1; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph1.pse1; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph1.pse3; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph1-nacl; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph1-nacl.pse1; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph1-nacl.pse3; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph2; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph10; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph10-nacl; fi if [ -n "" ]; then cd rism3d/phosphate && ./Run.ph20; fi (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 crg_reloc/cyt && ./Run.cyt.min) diffing min.out.save with min.out PASSED ============================================================== (cd crg_reloc/cyt && ./Run.cyt.md) diffing md.out.save with md.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.dist.type1) diffing dist.type1.out.save with dist.type1.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.dist.type3) diffing dist.type3.out.save with dist.type3.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.dist.type4) diffing dist.type4.out.save with dist.type4.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.dist.type5) diffing dist.type5.out.save with dist.type5.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.angle.type1) diffing angle.type1.out.save with angle.type1.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.angle.type2) diffing angle.type2.out.save with angle.type2.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.angle.type3) diffing angle.type3.out.save with angle.type3.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.angle.type4) diffing angle.type4.out.save with angle.type4.out PASSED ============================================================== (cd crg_reloc/misc && ./Run.mix) diffing mix.out.save with mix.out PASSED ============================================================== (cd crg_reloc/1-4elec && ./Run.opt0) diffing min.opt0.out.save with min.opt0.out PASSED ============================================================== (cd crg_reloc/1-4elec && ./Run.opt1) diffing min.opt1.out.save with min.opt1.out PASSED ============================================================== cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.test CLEANING CALCULATING TEST: 01_GenerateSnapshots CHECKING IN TEST: 01_GenerateSnapshots diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/src/mm_pbsa/Examples/01_GenerateSnapshots/test_com.crd.4.save with /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/src/mm_pbsa/Examples/01_GenerateSnapshots/test_com.crd.4 PASSED ============================================================== diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/src/mm_pbsa/Examples/01_GenerateSnapshots/test_lig.crd.4.save with /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/src/mm_pbsa/Examples/01_GenerateSnapshots/test_lig.crd.4 PASSED ============================================================== diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/src/mm_pbsa/Examples/01_GenerateSnapshots/test_rec.crd.4.save with /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/src/mm_pbsa/Examples/01_GenerateSnapshots/test_rec.crd.4 PASSED ============================================================== CALCULATING TEST: 02_MMPBSA_Stability ./Run.mmpbsa.test: Program error Makefile:890: recipe for target `test.mm_pbsa' failed make[2]: [test.mm_pbsa] Error 1 (ignored) 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 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb0 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2_saltcon DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_disp DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_shake_DFTB && ./Run.nma_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_dis_neg DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_method2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_qmmm_int0 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb5 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb7 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2_alpb && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/water && ./Run.water DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/water && ./Run.water_read_mdin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/water && ./Run.water_read_file DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md_hot_start DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_calc_mulliken DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_alpb DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_saltcon DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_link_atoms DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_telec DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM_MD DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme_qmewald DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_bigqmcut_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut_lowmem && ./Run.MG_QM_water_MM_MD DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake_qmshakeoff DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_min DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_dis_neg DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_method2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1_disp DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR DFTB SLKO files not found - Skipping Test... cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_DFTB DFTB SLKO files not found - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb ADF dftb program not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb_md ADF dftb program not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz ADF not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz_md ADF not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.template.lda-sz ADF not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g GAMESS not installed - Skipping Test... make sure that GMS_PATH points to the GAMESS installation directory cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g_md GAMESS not installed - Skipping Test... make sure that GMS_PATH points to the GAMESS installation directory cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.template.bp86_6-31g GAMESS not installed - Skipping Test... make sure that GMS_PATH points to the GAMESS installation directory cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g TeraChem not installed - Skipping Test... make sure that environment variable TeraChem points to the TeraChem installation and that the TeraChem executable is called terachem, that is, $TeraChem/terachem exists cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g_md TeraChem not installed - Skipping Test... make sure that environment variable TeraChem points to the TeraChem installation and that the TeraChem executable is called terachem, that is, $TeraChem/terachem exists cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.template.blyp_6-31g TeraChem not installed - Skipping Test... make sure that environment variable TeraChem points to the TeraChem installation and that the TeraChem executable is called terachem, that is, $TeraChem/terachem exists cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g GAUSS_EXEDIR is not set - Skipping Test... If you have g03 or g09 installed, make sure the environment variable GAUSS_EXEDIR is set and g03 or g09 is in that directory cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g_md GAUSS_EXEDIR is not set - Skipping Test... If you have g03 or g09 installed, make sure the environment variable GAUSS_EXEDIR is set and g03 or g09 is in that directory cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.template.blyp_sto-3g GAUSS_EXEDIR is not set - Skipping Test... If you have g03 or g09 installed, make sure the environment variable GAUSS_EXEDIR is set and g03 or g09 is in that directory cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g Orca not installed - Skipping Test... make sure that environment variable ORCAHOME points to the Orca installation and that the Orca executable is called orca, that is, $ORCAHOME/orca exists cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g_md Orca not installed - Skipping Test... make sure that environment variable ORCAHOME points to the Orca installation and that the Orca executable is called orca, that is, $ORCAHOME/orca exists cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.template.blyp_6-31g Orca not installed - Skipping Test... make sure that environment variable ORCAHOME points to the Orca installation and that the Orca executable is called orca, that is, $ORCAHOME/orca exists 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/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g Orca not installed - Skipping Test... make sure that environment variable ORCAHOME points to the Orca installation and that the Orca executable is called orca, that is, $ORCAHOME/orca exists cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g.MechEm /bin/sh: ./Run.aladip.hf_sto-3g.MechEm: No such file or directory Makefile:532: recipe for target `test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 127 (ignored) cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g Orca not installed - Skipping Test... make sure that environment variable ORCAHOME points to the Orca installation and that the Orca executable is called orca, that is, $ORCAHOME/orca exists cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Orca not installed - Skipping Test... make sure that environment variable ORCAHOME points to the Orca installation and that the Orca executable is called orca, that is, $ORCAHOME/orca exists cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g TeraChem not installed - Skipping Test... make sure that environment variable TeraChem points to the TeraChem installation and that the TeraChem executable is called terachem, that is, $TeraChem/terachem exists cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g.MechEm /bin/sh: ./Run.aladip.hf_sto-3g.MechEm: No such file or directory Makefile:532: recipe for target `test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 127 (ignored) cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g TeraChem not installed - Skipping Test... make sure that environment variable TeraChem points to the TeraChem installation and that the TeraChem executable is called terachem, that is, $TeraChem/terachem exists cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g.MechEm /bin/sh: ./Run.nma-spcfw-15.hf_sto-3g.MechEm: No such file or directory Makefile:532: recipe for target `test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 127 (ignored) cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.aladip.hf_sto-3g GAUSS_EXEDIR is not set - Skipping Test... If you have g03 or g09 installed, make sure the environment variable GAUSS_EXEDIR is set and g03 or g09 is in that directory cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.nma-spcfw-15.hf_sto-3g GAUSS_EXEDIR is not set - Skipping Test... If you have g03 or g09 installed, make sure the environment variable GAUSS_EXEDIR is set and g03 or g09 is in that directory 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 export TESTsander='../../bin/pmemd'; cd 4096wat && ./Run.pure_wat diffing mdout.pure_wat.save with mdout.pure_wat PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd 4096wat && ./Run.pure_wat_nmr_temp_reg diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd 4096wat && ./Run.vrand diffing mdout.vrand.save with mdout.vrand PASSED ============================================================== export TESTsander='../../bin/pmemd'; 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 ============================================================== export TESTsander='../../bin/pmemd'; cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd cytosine && ./Run.cytosine diffing cytosine.out.save with cytosine.out PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd dhfr && ./Run.dhfr diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd dhfr && ./Run.dhfr.min diffing mdout.dhfr.min.save with mdout.dhfr.min PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd dhfr && ./Run.dhfr.noshake diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd variable_14 && ./Run.variable_14_ntb1 diffing variable_14_ntb1.mdout.save with variable_14_ntb1.mdout PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd variable_14 && ./Run.variable_14_igb1 diffing variable_14_igb1.mdout.save with variable_14_igb1.mdout PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd trx && ./Run.trx diffing mdout.trx.save with mdout.trx PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd trx && ./Run.trx.cpln.pmemd diffing mdout.trx.cpln.pmemd.save with mdout.trx.cpln.pmemd PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd circ_dna && ./Run.circdna diffing mdout.circdna.save with mdout.circdna PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gb2_trx && ./Run.trxox.nogbsa && ./Run.trxox.nogbsa prmtop_an diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gb7_trx && ./Run.trxox_md diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gb8_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== export TESTsander='../../bin/pmemd'; 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 ============================================================== export TESTsander='../../bin/pmemd'; cd alpb_trx && ./Run.trxox.nogbsa diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gb1_cox2 && ./Run.cox2 diffing cox2.out.save with cox2.out PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gbsa_xfin && ./Run.gbsa diffing mdout.gbsa.save with mdout.gbsa PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd tip4p && ./Run.tip4p diffing mdout.tip4p.save with mdout.tip4p PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd tip4p && ./Run.tip4p_nve diffing mdout.tip4p_nve.save with mdout.tip4p_nve PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd tip5p && ./Run.tip5p diffing mdout.tip5p.save with mdout.tip5p PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd tip5p && ./Run.tip5p_nve diffing mdout.tip5p_nve.save with mdout.tip5p_nve PASSED ============================================================== export TESTsander='../../../../bin/pmemd'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== export TESTsander='../../../../bin/pmemd'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== export TESTsander='../../../../bin/pmemd'; cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== export TESTsander='../../../../bin/pmemd'; 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 ============================================================== export TESTsander='../../../../bin/pmemd'; 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 ============================================================== export TESTsander='../../../../bin/pmemd'; 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 ============================================================== export TESTsander='../../../../bin/pmemd'; 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='../../bin/pmemd'; cd amd && ./Run.dhfr.amd3 diffing mdout.dhfr.amd3.save with mdout.dhfr.amd3 PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd gact_ips && ./Run.ips diffing mdout.ips.save with mdout.ips PASSED ============================================================== export TESTsander='../../bin/pmemd'; cd csurften && ./Run.csurften_z-dir diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir PASSED ============================================================== export TESTsander='../../bin/pmemd'; 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 amoeba_wat1 && ./Run.amoeba_wat1.pmemd | WARNING: Stack usage limited by a hard resource limit of 2097152 bytes! | If segment violations occur, get your sysadmin to increase the limit. diffing amoeba_wat1.pmemd.out.save with amoeba_wat1.pmemd.out PASSED ============================================================== cd amoeba_wat2 && ./Run.amoeba_wat2.pmemd | WARNING: Stack usage limited by a hard resource limit of 2097152 bytes! | If segment violations occur, get your sysadmin to increase the limit. diffing amoeba_wat2.pmemd.out.save with amoeba_wat2.pmemd.out PASSED ============================================================== cd amoeba_wat2 && ./Run.ntpverlet.pmemd | WARNING: Stack usage limited by a hard resource limit of 2097152 bytes! | If segment violations occur, get your sysadmin to increase the limit. STOP PMEMD Terminated Abnormally! diffing ntpverlet.pmemd.save with ntpverlet.pmemd possible FAILURE: check ntpverlet.pmemd.dif ============================================================== cd amoeba_gb1 && ./Run.amoeba_gb1.pmemd | WARNING: Stack usage limited by a hard resource limit of 2097152 bytes! | If segment violations occur, get your sysadmin to increase the limit. STOP PMEMD Terminated Abnormally! diffing mdout.amoeba_gb1.pmemd.save with mdout.amoeba_gb1.pmemd possible FAILURE: check mdout.amoeba_gb1.pmemd.dif ============================================================== cd amoeba_jac && ./Run.amoeba_jac.pmemd | WARNING: Stack usage limited by a hard resource limit of 2097152 bytes! | If segment violations occur, get your sysadmin to increase the limit. diffing amoeba_jac.pmemd.mdout.save with amoeba_jac.pmemd.mdout PASSED ============================================================== cd amoeba_formbox && ./Run.amoeba_formbox.pmemd | WARNING: Stack usage limited by a hard resource limit of 2097152 bytes! | If segment violations occur, get your sysadmin to increase the limit. diffing amoeba_formbox.pmemd.mdout.save with amoeba_formbox.pmemd.mdout PASSED ============================================================== cd amoeba_softcore && ./Run.amoeba_softcore.pmemd | WARNING: Stack usage limited by a hard resource limit of 2097152 bytes! | If segment violations occur, get your sysadmin to increase the limit. diffing mdout.amoeba_softcore.pmemd.save with mdout.amoeba_softcore.pmemd PASSED ============================================================== Finished serial test suite for Amber 12 at Tue, Apr 03, 2012 12:22:29 AM. make[2]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/test' 476 file comparisons passed 3 file comparisons failed 1 tests experienced errors Test log file saved as /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/logs/test_amber_serial/2012-04-02_23-30-39.log Test diffs file saved as /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/logs/test_amber_serial/2012-04-02_23-30-39.diff