[gmx-users] Pressure in NPT simulation

Mishelle Oña samimishu at hotmail.com
Sun Mar 19 20:34:53 CET 2017

Hello Justin, thanks for your help. The simulation has 2500000 steps (5000ps).


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Sunday, March 19, 2017 2:20 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Pressure in NPT simulation

On 3/19/17 3:17 PM, Mishelle Oña wrote:
> Hello,
> I have a question concerning pressure. I runned a NPT simulation with the following parameters:
> ; Pressure coupling
> Pcoupl                   = Berendsen
> Pcoupltype               = Isotropic
> tau_p                    = 1.01325

This is a rather odd value of tau_p.  Remember this is time, not bar.

> compressibility          = 4.5e-5
> ref_p                    = 1.01325
> When analyzing the average pressure using g_energy I got this results:
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                   -128613        9.9    363.247   -65.2445  (kJ/mol)
> Kinetic En.                 24189.2        1.4    242.381   -6.10124  (kJ/mol)
> Total Energy                -104424         11    440.485   -71.3457  (kJ/mol)
> Temperature                 300.544      0.018    3.01152 -0.0758065  (K)
> Pressure                    323.536       0.65    244.361   -3.94119  (bar)
> I wonder why the simulation cannot descent to the ref_p value. It is a system of a polymer in a box full of water.
>  Thanks for the answer and help.

How long was the simulation?  Have you read
http://www.gromacs.org/Documentation/Terminology/Pressure and/or any of the
million or so posts where people wonder about weird values of pressure? :)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
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