[gmx-users] NPT simulation stage

[Justin Lemkul]

On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote:
> hi GMX users
> please help me
> i want to simulate protein-ligand complex by gromacs4.6.5
> when i repeat NPT simulation stage  many times,  simulation results are very different for the pressure average.I sincerely thank you for your guidance
>

Pressure is probably the most ill-defined quantity in MD simulations.  It can 
fluctuate dramatically.  Without the actual numbers, it's hard to comment, but 
issues related to pressure have been discussed extensively over the list in the 
past and there is useful information in 
http://www.gromacs.org/Documentation/Terminology/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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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