On 10/27/13 12:05 PM, shahab shariati wrote:
Dear Tsjerk Wassenaar
Very very thanks for your reply.
I used trjconv -pbc mol.
pbc problem was solved only for lipid molecules.
When I see new trajectory by vmd, there are some problesm about drug
molecule.
https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx
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),
alternately.
On the other hand, drug molecule is in region (1)in some frames and is
in region (4) in other frames.
Please tell me how to fix it? Is this issue (about drug molecule) pbc
problem?
As has already been stated several times, there is no problem at all. The
outcome is completely normal, and there are not discrete regions (1) and (4).
It is a continuous block of water via PBC. The molecule can freely diffuse
throughout it.
-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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