[gmx-users] obtaining .gro timeframe

[Justin Lemkul]

On 7/1/14, 9:08 PM, Chetan Mahajan wrote:
> Thanks, Justin. Are you saying, the coordinates in .gro  file extracted
> from xtc trajectory are not wrapped, whereas those in the .gro file
> generated at the end of gromacs MD run are wrapped in the box?
>

Yes, unless you've manipulated the trajectory in some way with trjconv beforehand.

> Now I have a question:  the negative coordinates that are present in the
> following text are from .gro file (generated at the end of MD run), whereas
> positive ones are from .gro file obtained using trjconv on xtc.
>

Either way, it's a periodicity effect.  Molecules are made 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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