[gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/15/14 4:52 AM, shahab shariati wrote:
> Dear Tsjerk
>
> Thanks for your reply.
>
> I think that there is another problem, except for visualization.
>
> I obtained the Z coordinate (along the bilayer normal) of the center of
> mass of the 4 drug molecules (violet, blue, red and green lines) and
> DPPC lipid bilayer (black line) as a function of simulation time, using
> g_traj tool.
>
>   The related figure is in following link:
>
>
>
> https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0
>
>   This Figure is not normal and usual.
>

Sure it is.  It may just not be the aesthetically pleasing output you want.

>   What is your opinion about this issue?
>

You're asking the same questions that were answered last week:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092153.html

Yes, your plot is normal.  Again, as I said in the linked message, there is no 
"side" in a periodic system.  You have a continuous water layer.  Your molecules 
simply diffuse around in it.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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