AMBER Archive (2004)

Subject: Re: AMBER: non-isotropic pressure scaling

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Wed Apr 14 2004 - 14:21:54 CDT

hi guys,

here are the final results and a short summary. test was performed on
dhfr benchmark, 100 steps, printout every single step. ntb was changed
to 2 (constant pressure) and ntp to 2 (nonisotropic scaling)

- sander7 and pmemd-3.1 produce exactly the same numbers when
amber7_compat = 1 is used

- pmemd-3.1 results in nocit or amber 6 cit mode are the same. when
compared to sander7 results there are some differences:

sander 7 averages for 100 steps:
================================
  NSTEP = 100 TIME(PS) = 510.150 TEMP(K) = 299.05 PRESS = -148.5
  Etot = -57762.4772 EKtot = 14005.7262 EPtot = -71768.2034
  BOND = 476.0346 ANGLE = 1266.5567 DIHED = 987.0423
  1-4 NB = 537.4913 1-4 EEL = 6646.8490 VDWAALS = 8324.2655
  EELEC = -90006.4428 EHBOND = 0.0000 RESTRAINT = 0.0000
  EKCMT = 6124.0382 VIRIAL = 6864.3012 VOLUME = 230807.7450
                                              Density = 1.0139
  Ewald error estimate: 0.7657E-04

pmemd 3.1 cit (amber 6) averages for 100 steps:
===============================================
  NSTEP = 100 TIME(PS) = 510.150 TEMP(K) = 299.73 PRESS = -167.65
  Etot = -57738.9175 EKtot = 14038.5819 EPtot = -71777.4994
  BOND = 474.3691 ANGLE = 1264.2984 DIHED = 987.3340
  1-4 NB = 539.1834 1-4 EEL = 6650.9716 VDWAALS = 8340.4301
  EELEC = -90034.0861 EHBOND = 0.0000 CONSTRAINT = 0.0000
  EKCMT = 6125.7684 VIRIAL = 6961.3817 VOLUME = 230726.5228
                                              Density = 1.0143
  Ewald error estimate: 0.7775E-04

the question is whether the differences significant and whether they
will vanish or propagate for longer md runs.

however, when amber7_compat = 1 is used, nonisotropic pressure scaling
(ntp=2) SEEMS to work fine.

the only required change to the pmemd-3.1 source is commenting out
appropriate part of the mdin_ctrl_dat.f90 file where input is tested for
NTP .eq. 2 (approximately lines 388-393 of that file). all other files
already contain the necessary routines (you can check runmd*.f90)

thanks to all people who helped me when solving this problem. regards, 

-- 
Lubos
_@_"
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