[gmx-users] monitor the size of the computational box

Justin Lemkul jalemkul at vt.edu
Mon Jul 6 17:17:26 CEST 2015

On 7/6/15 11:15 AM, Giannis Gl wrote:
> Dear all,
> I would like to ask what is the best way to monitor the size of the
> computational box (i.e. the volume)
> during a simulation. I know that it must stay constant during the
> simulation but, in my case, it seems that it doesn't.

The box is only constant with NVE or NVT, but with NPT it will not be.

> There is an error poping up when I try to use the gmx hbond tool,
> specifically "Your computational box has shrunk too much",
> and I've read that it is reccomended to plot the box volume as a function
> of time. How can I do this?

Extract it from the .edr file.



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


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