# [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).

Mishelle

________________________________
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

--
==================================================

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
http://mackerell.umaryland.edu/~jalemkul
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul>

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

==================================================
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>
www.gromacs.org
This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page.

Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists>
www.gromacs.org
The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them:

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
gromacs.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
maillist.sys.kth.se
gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users

```