On 10/27/13 8:16 AM, shahab shariati wrote:
Dear Justin
I want to study translocation of drug molecule in lipid bilayer.
My gro file after minimization is em2.gro.
After NPT-MD simulation, I obtained npt.gro and 0.xtc files.
When I see trajectory by vmd, there are some things abnormal.
I guess there is pbc problem.
I attached these 3 files. Please after viewing them, tell me is my guess
true.
If yes, please guide me how to fix it. If no, please tell me what is
problem?
https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro
https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro
https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc
Images are better, especially ones that don't have to be downloaded. I'm not
going to download a potentially large .xtc file, sorry.
-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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