[gmx-users] Pressures after NPT

[Justin Lemkul]

On 8/6/14, 4:54 AM, ibrahim khalil wrote:
> dear gromacs users, I did an NPT equilibration of 100ps with a reference
> pressure of 1bar. After the equilibration, my average pressure was 1.2 bar.
> But when I started my production run (with a reference pressure of 1 bar)
> my pressure was rising (and falling) again. for the first 50 ps, the
> average pressure was -7.2 bar. Then after a 100ps of production run the
> pressure was -0.84 bar.
>
> I have two questions regrading this-
>
> 1. Does negative pressure mean anything wrong with my system? or should I
> just take the magnitude of my pressure?
>

Positive and negative correspond to expansion and contraction.

> 2. After the NPT my average pressure was rising again(but eventually came
> close to its reference value after some time), should it happen in a stable
> simulation?
>

Pressure fluctuates wildly in a simulation.  See 
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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