[gmx-users] pbc problem

[Justin Lemkul]

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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