[gmx-users] PBC problem in bilayer system

Justin Lemkul jalemkul at vt.edu
Sun Sep 14 14:46:27 CEST 2014

On 9/14/14 8:43 AM, shahab shariati wrote:
> Dear Justin
> Thanks for your reply.
> I inserted 4 drug molecules in close vicinity to the membrane surface
> in water phase, in one side of bilayer (for example, top). In the
> different frames of trajectory, some of drug molecules (one or two
> drug molecules) are seen in other side of bilayer (bottom).  I really
> do not know what thing has to be translated. Should I shift all
> components of my system (DPPC, drug, and water molecules) along z or
> only drug molecules?

Translate the whole system.

> The dimensions of my system in final gro file are as follows:
>   6.46063   6.57889   8.30034
> Based on your reply (The exact magnitude depends on the dimensions of the
> system), should I use following command:
> trjconv –trans 6.46063   6.57889   8.30034

If you used pressure coupling, no, because the box dimensions will change over 
time.  Moreover, you do not want to change x and y.  As I said before, you want 
to translate along z.  Try a few values and see if you get a reasonable result.



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


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