[gmx-users] Pressure Coupling in GROMACS

[Justin Lemkul]

On 6/8/15 9:53 AM, Jashimuddin Ashraf wrote:
> Thanks for your reply Dr. Lemkul. I came across some of the widely
> fluctuating pressures before but the average pressure was more or less
> close to the target values previously (even though the instantaneous values
> varied quite a lot).
>
> But in my case, the average pressure is far different from the target
> values.
>

Please provide the actual output from gmx energy.  "Far different" depends 
entirely upon context, e.g. the fluctuations themselves.

> The pressure curve I am generating using g_energy is attached here.
>

The list does not accept attachments.

>
> PS. I have 2 carbon nanotubes in my system; one of them is entirely frozen
> and the other one is entirely free. Is anything wrong with my system?
>

Freezing can cause artifacts with pressure coupling.  See notes in the manual.

-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

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