AMBER Archive (2006)

Subject: AMBER: amber8 bugfix effects

From: kawamura_hiro_at_riken.jp
Date: Wed May 24 2006 - 03:17:32 CDT

Dear All,

I install amber8 with bugfix.all. Then, Results of Output file(mdout)
change different from before applying bugfix.

follings are input file and results.

###############################################
  input file (mdin)
###############################################

Molecular Dynamics
 &cntrl
   TIMLIM = 999999, IMIN = 0, NMROPT = 0,
   NTX = 5, IREST = 1, NTRX = 1,
   NTXO = 1, NTPR = 100, NTWR = 0, IWRAP = 0,
   NTWX = 0, NTWV = 0, NTWE = 0,
   IOUTFM = 0, NTWPRT = 0,
   NTF = 2, NTB = 0, DIELC = 1.000, IGB = 0,
   GBSA = 0,
   SCNB = 2.000, SCEE = 1.200, CUT = 999.0,
   IPOL = 0,
   IBELLY = 0, NTR = 0,
   NSTLIM = 100, NSCM = 0,
   T = 0.0000, DT = 0.00100,
   TEMP0 =300.000, TEMPI = 0.000, IG = 71277,
   NTT = 0, TAUTP = 0.200, VLIMIT = 0.000,
   NTP = 0, PRES0 = 1.000, COMP = 44.600, TAUP = 0.200,
   NTC = 2, TOL = 0.00050,
   JFASTW = 0,
   IVCAP = 0, FCAP = 1.500,
   ISCALE = 0, NOESKP = 1, IPNLTY = 1, MXSUB = 1,
   SCALM = 100, PENCUT = 0.100, TAUSW = 0.100,
 &end

###############################################
  output file (mdout) without bugfix
###############################################

 NSTEP = 100 TIME(PS) = 120.100 TEMP(K) = 299.89 PRESS = 0.0
 Etot = -12549.2500 EKtot = 3431.9570 EPtot = -15981.2071
 BOND = 155.2736 ANGLE = 333.2934 DIHED = 279.9651
 1-4 NB = 196.5001 1-4 EEL = 3085.5627 VDWAALS = 1751.5865
 EELEC = -21783.3883 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

      A V E R A G E S O V E R 100 S T E P S
 NSTEP = 100 TIME(PS) = 120.100 TEMP(K) = 302.25 PRESS = 0.0
 Etot = -12549.3042 EKtot = 3459.0328 EPtot = -16008.3371
 BOND = 149.2596 ANGLE = 385.4573 DIHED = 289.3220
 1-4 NB = 186.9813 1-4 EEL = 3046.3061 VDWAALS = 1766.3508
 EELEC = -21832.0141 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S
 NSTEP = 100 TIME(PS) = 120.100 TEMP(K) = 2.79 PRESS = 0.0
 Etot = 0.3579 EKtot = 31.9626 EPtot = 31.9198
 BOND = 10.3496 ANGLE = 17.0561 DIHED = 4.2182
 1-4 NB = 5.4555 1-4 EEL = 17.7030 VDWAALS = 18.6380
 EELEC = 31.3340 EHBOND = 0.0000 RESTRAINT = 0.0000
|E(PBS) = 0.3324

###############################################
  output file (mdout) apply bugfix
###############################################
 NSTEP = 100 TIME(PS) = 120.100 TEMP(K) = 299.89 PRESS = 0.0
 Etot = -12544.9131 EKtot = 3431.9570 EPtot = -15976.8701
 BOND = 155.2736 ANGLE = 333.2934 DIHED = 279.9651
 1-4 NB = 196.5001 1-4 EEL = 3085.5627 VDWAALS = 1751.5862
 EELEC = -21783.3748 EHBOND = 0.0000 RESTRAINT = 4.3237
 EAMBER (non-restraint) = -15981.1938
 ------------------------------------------------------------------------------

      A V E R A G E S O V E R 100 S T E P S
 NSTEP = 100 TIME(PS) = 120.100 TEMP(K) = 302.25 PRESS = 0.0
 Etot = -12621.6512 EKtot = 3459.0329 EPtot = -16080.6841
 BOND = 149.2596 ANGLE = 385.4573 DIHED = 289.3220
 1-4 NB = 186.9813 1-4 EEL = 3046.3061 VDWAALS = 1750.5246
 EELEC = -21893.1231 EHBOND = 0.0000 RESTRAINT = 4.5881
 EAMBER (non-restraint) = -16085.2722
 ------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S
 NSTEP = 100 TIME(PS) = 120.100 TEMP(K) = 2.79 PRESS = 0.0
 Etot = 32.0935 EKtot = 31.9626 EPtot = 18.4361
 BOND = 10.3496 ANGLE = 17.0562 DIHED = 4.2182
 1-4 NB = 5.4555 1-4 EEL = 17.7030 VDWAALS = 0.1067
 EELEC = 11.0301 EHBOND = 0.0000 RESTRAINT = 0.2945
 EAMBER (non-restraint) = 18.1417
|E(PBS) = 32.1449

###############################################

Result of "RESTRAINT","EANBER","Etot" and "EPtot" are changed.
The results of after applying bugfix are corrects?

Sincerery　Yours,
H. Kawamura

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