[gmx-users] obtaining .gro timeframe

[Justin Lemkul]

On 7/2/14, 6:45 PM, Chetan Mahajan wrote:
> Thanks a lot, Justin. It's much clearer, but one last question: If the
> coordinates in sample.gro extracted from xtc trajectory using trjconv (
> without any application of pbc) are unwrapped, why almost all of them
> happen to lie in the box, as can be seen in the following snapshot? I would
> expect many of them scattered in space, beyond original box?
>
> https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va
>
> Dark blue line is the box boundary.
>

A central unit cell is still maintained; it's just that the molecules aren't 
necessarily whole.

-Justin

-- 
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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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