AMBER Archive (2005)

Subject: AMBER: doubt on the value of Pressure on MD run

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Tue Jul 12 2005 - 03:21:07 CDT

Dear Amber Users,
                  i have did MD simulation for organic molecules using
Amber7. the following input i hvae used for the MD simulation.

MD_simulation of 64_PIMB
 &cntrl
       
   imin = 0, irest = 0, ntx = 1,
       
   ntt = 1, temp0 = 454.0, tautp = 1.0,
       
   ntp = 2, pres0 = 1.0, taup = 0.2,
       
   ntb = 2, ntc = 1, ntf = 1,
       
   nstlim = 300000,
       
   tempi = 454.0, dt = .001,
       
   cut = 10.0,
       
   ntpr = 200, ntwx = 200,
       
 &end

the results of the MD run as follows

NSTEP = 300000 TIME(PS) = 360.000 TEMP(K) = 458.62 PRESS = 84.5
 Etot = 9125.9326 EKtot = 8922.7843 EPtot = 203.1483
 BOND = 3155.1958 ANGLE = 3954.8001 DIHED = 2722.0354
 1-4 NB = 2241.2389 1-4 EEL = -9234.5666 VDWAALS = -3937.0160
 EELEC = 1301.4608 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 84.3661 VIRIAL = -51.7373 VOLUME = 74581.5314
                                                Density = 1.0329
 Ewald error estimate: 0.1451E-03

i have doubt on the value of the pressure. i have given 1 atm as a
reference pressure in the input but in the final results the value is
about 85 atm or so..is it correct..

thanks in advance...anand

ANANDA RAMA KRISHNAN .S
PhD Student
c/o. Dr. Rudolf Friedemann
Department of organic chemistry
Martin Luther university
Kurt-mothes-str.2
D-06120 Halle (saale),Germany
e-mail: ananda.selvaraj_at_chemie.uni-halle.de
Ph(lab) : (+int) 345 - 5525683
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