[gmx-users] pbc problem

[Justin Lemkul]

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

-- 
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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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