[gmx-users] Pressure in NPT simulation

[Justin Lemkul]

On 3/19/17 3:34 PM, Mishelle Oña wrote:
> Hello Justin, thanks for your help. The simulation has 2500000 steps (5000ps).
>

Depending on what your polymer is and how it behaves (entanglement, etc) it may 
take a long time to converge.  For a very simple system, 5 ns should be enough. 
For a polymer, I don't know what you should expect.

-Justin

> 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

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

==================================================