AMBER Archive (2005)

Subject: AMBER: small target pressure in constant pressure dynamics

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Thu Apr 14 2005 - 16:37:49 CDT

Hi, I am doing a constant pressure simulation of a peptide bound with
a protein after a constant volume simulation with Amber 8.0. The
average pressure is only 0.6 bar which I believe is considerably low
comparing with the target pressure (at 1 bar).

Eric
 
&cntrl
  imin=0,
  irest = 1,
  ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1
  cut = 10,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  tempi = 300.0
  temp0 = 300.0
  ntt = 3,gamma_ln = 1.0
  nstlim = 5000000, dt = 0.002
  ntpr = 1000, ntwx = 1000, ntwr = 1000
 /

...
      A V E R A G E S O V E R 5000000 S T E P S

  NSTEP = 5000000 TIME(PS) = 12020.000 TEMP(K) = 299.96 PRESS = 0.6
  Etot = -34377.4750 EKtot = 9862.0683 EPtot = -44239.5433
  BOND = 694.9707 ANGLE = 1795.1316 DIHED = 2243.9312
  1-4 NB = 826.7005 1-4 EEL = 10979.3095 VDWAALS = 3445.1211
  EELEC = -64224.7078 EHBOND = 0.0000 RESTRAINT = 0.0000
  EKCMT = 3605.6219 VIRIAL = 3603.6831 VOLUME = 153249.1291
                                                    Density = 1.0655
  Ewald error estimate: 0.8293E-04
 ------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S

  NSTEP = 5000000 TIME(PS) = 12020.000 TEMP(K) = 2.30 PRESS = 215.7
  Etot = 133.7865 EKtot = 75.7401 EPtot = 108.9025
  BOND = 22.1261 ANGLE = 32.8074 DIHED = 21.3345
  1-4 NB = 12.1688 1-4 EEL = 42.6810 VDWAALS = 91.5482
  EELEC = 155.0986 EHBOND = 0.0000 RESTRAINT = 0.0000
  EKCMT = 45.9191 VIRIAL = 715.5470 VOLUME = 686.3206
                                                    Density = 0.0044
  Ewald error estimate: 0.6189E-04
 ------------------------------------------------------------------------------
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