[gmx-users] Pressure in NPT simulation

[Mishelle Oña]

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

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

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