[gmx-users] problem in g_membed

Justin Lemkul jalemkul at vt.edu
Tue Jul 2 18:10:37 CEST 2013

On Tue, Jul 2, 2013 at 11:36 AM, Pavithra <meetpavithramsc at gmail.com> wrote:

> Dear gromacs users,
> I'm new to simulation.
> I'm running a membrane protein simulation with gromacs and am following
> KALP tutorial.
> I skipped inflategro and used g_membed command to insert my protein complex
> into POPE membrane.
> I followed the tutorial and got the work done but with a peculiar error.
> few amino acid's atoms were protruding above the box were sliced and been
> added to the other side of the box..
> is this possible?.

Not only is it possible, it is expected.  What you've described is the fact
that your box is of insufficient size to accommodate your protein.  As a
consequence, PBC re-wraps the image of the protein such that it is within
the unit cell (since there is no such thing as "inside" or "outside" an
infinite system.

> since its the first time I don't know want information I have to provide.
> Please let me know if I have to send the mdp file or the command i've used.

When reporting problems, in general, such information is absolutely
necessary.  In this case, probably not.




Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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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