[gmx-users] Pressure problem in EM simulation

Mishelle Oña samimishu at hotmail.com
Sun Mar 19 02:18:50 CET 2017

Thanks for your answer Justin.

Another question for the same simulation. I got this values of potential energy:

Average> -127776



Tot-Drift> -32877.9

I think the RMSD is way too high. What do you think?

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: Saturday, March 18, 2017 8:06 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Pressure problem in EM simulation

On 3/18/17 9:00 PM, Mishelle Oña wrote:
> Hello!
> I have a question about pressure in EM simulation. I am using Steepest descent method in a water polymer system. My pressure gets this value:
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                   -2843.38         65    162.655   -446.059  (bar)
> The pressure value is very weird. Is this normal? or I am doing something wrong?

There's no barostat or velocities during EM so the value you see has no real



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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