[gmx-users] pbc problem
jalemkul at vt.edu
Thu Oct 24 17:01:27 CEST 2013
On 10/24/13 10:57 AM, shahab shariati wrote:
> Dear Mark
> Thank for your reply.
> If I show my system as 4 regions, my system before equilibration is as fallows:
> region (1): water + drug
> region (2): top leaflet of bilayer
> region (3): bottom leaflet of bilayer
> region (4): water
> After equilibration, drug molecule exits region (1) and enters region (4).
> Please tell me how to fix it? Which options of trjconv are appropriate
> for this problem?
So the drug diffused within a continuous block of solvent, is that a problem?
It shouldn't be, since the system is periodic. In some cases, trjconv magic
doesn't work because it shouldn't.
Justin A. Lemkul, Ph.D.
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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