#
# Amber Ubuntu Installation Output File
# For more information, see http://www.somewhereville.com/?p=345
# Damian Allis, damian@somewhereville.com, www.somewhereville.com
#
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
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
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE:  check stem.dip.o.dif
==============================================================
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
==============================================================
diffing mdcrd.out.save with mdcrd.out
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.jar
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 bintraj && ./Run.bintraj
diffing nc_headers.save with nc_headers
PASSED
==============================================================
cd gb_rna && ./Run.gbrna
diffing mdout.gbrna.save with mdout.gbrna
PASSED
==============================================================
cd gb_rna && ./Run.gbrna.min
diffing mdout.gbrna.min.save with mdout.gbrna.min
PASSED
==============================================================
cd gb_rna && ./Run.gbrna.ln
diffing mdout.gbrna.ln.save with mdout.gbrna.ln
PASSED
==============================================================
cd gb_rna && ./Run.gbrna.ips
diffing mdout.gbrna.ips.save with mdout.gbrna.ips
PASSED
==============================================================
cd gb_rna && ./Run.gbrna.sgld
diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld
PASSED
==============================================================
cd gbsa_xfin && ./Run.gbsa
diffing mdout.gbsa.save with mdout.gbsa
PASSED
==============================================================
cd circ_dna && ./Run.circdna
diffing mdout.circdna.save with mdout.circdna
PASSED
==============================================================
cd gb2_trx && ./Run.trxox
diffing mdout.trxox.save with mdout.trxox
PASSED
==============================================================
cd gb7_trx && ./Run.trxox
diffing mdout.trxox.save with mdout.trxox
PASSED
==============================================================
cd gb7_trx && ./Run.trxox_md
diffing mdout.trxox_md.save with mdout.trxox_md
PASSED
==============================================================
cd alpb_trx && ./Run.trxox
diffing mdout.trxox.save with mdout.trxox
PASSED
==============================================================
cd cnstph && ./Run.cnstph
diffing mdout.save with mdout
PASSED
==============================================================
diffing cpout.save with cpout
PASSED
==============================================================
cd gb1_cox2 && ./Run.cox2
diffing cox2.out.save with cox2.out
PASSED
==============================================================
cd LES_noPME && ./Run.LESmd
SANDER: LES MD gas phase
diffing md.out.save with md.out
PASSED
==============================================================
cd LES_noPME && ./Run.LESmd.rdiel
SANDER: LES MD gas phase rdiel
diffing md.rdiel.out.save with md.rdiel.out
PASSED
==============================================================
cd LES && ./Run.PME_LES
 
  Amber 8 ADDLES and SANDER.LES test: 
 
addles:
diffing output_addles.save with output_addles
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE:  check output_addles.dif
==============================================================
diffing LES.crd.save with LES.crd
PASSED
==============================================================
diffing LES.prmtop.save with LES.prmtop
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE:  check LES.prmtop.dif
==============================================================
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
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE:  check addles.out.dif
==============================================================
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
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE:  check addles.out.dif
==============================================================
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
awk: cannot open /test/ndiff.awk (No such file or directory)
possible FAILURE:  check amoeba_jac.mdout.dif
==============================================================
cd amoeba_formbox && ./Run.amoeba_formbox
diffing amoeba_formbox.mdout.save with amoeba_formbox.mdout
PASSED
==============================================================
cd ncsu && ./run-serial.sh
>>>>>>> doing 'abmd_ANALYSIS'
diffing save/mdout with mdout
PASSED
==============================================================
diffing save/monitor.txt with monitor.txt
PASSED
==============================================================
>>>>>>> doing 'abmd_FLOODING'
diffing save/mdout with mdout
PASSED
==============================================================
diffing save/monitor.txt with monitor.txt
PASSED
==============================================================
diffing umbrella.save.ncdump with umbrella.ncdump
PASSED
==============================================================
>>>>>>> doing 'abmd_UMBRELLA'
diffing save/mdout with mdout
PASSED
==============================================================
diffing save/monitor.txt with monitor.txt
PASSED
==============================================================
>>>>>>> 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 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
PASSED
==============================================================
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
PASSED
==============================================================
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'