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
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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