[gmx-users] Protein drifting out of the box.

[Justin Lemkul]

On 8/19/14, 12:45 PM, Dawid das wrote:
> Dear Gromacs experts,
>
> In my MD simulation I noticed that protein drifts toward one of the faces
> of cubic solvation box. Now I use periodic boundary conditions but one of
> the residues sticks out of solvation box. My general question is: is it
> okay or should I be aware of such a system behaviour?
>

http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

Point #3.

-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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