[gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/11/14 8:01 AM, shahab shariati wrote:
> Dear gromacs users
>
> When I see trajectory file using vmd, there is state showed in following link:
>
> https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0
>
> in initial structure, all 4 drugs were  inserted in water phase, in one side of
> bilayer.
>
> Is this state normal?
>

Yes, because there's no such thing as a "side" in a periodic system.  You have a 
water layer that is continuous in z, so the molecules are free to diffuse around 
as they please.  It may not be possible to re-image the trajectory such that all 
of the drug molecules are positioned in the same region in the unit cell.  You 
can try the translation options of trjconv (in conjunction with -pbc mol) to try 
to shift the system up or down to get everything to fit, but then of course the 
lipids can jump around.  Perhaps additional calls to trjconv can account for 
that (i.e. another round of -pbc nojump after translating).

-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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