[gmx-users] pbc problem

[Justin Lemkul]

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

-- 
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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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