[gmx-users] Non Periodic Coordinate File

[Justin Lemkul]

On 8/20/15 5:59 PM, ANAND AMITKUMAR Dharia wrote:
> Hello,
>
> I was wondering if it was possible to create a non-periodic coordinate file
> using trjconv or some other gromacs program on a trajectory file. I would
> like to use coordinate data to calculate displacement in order to compute a
> crosscorrelation between molecules, however, with the jumps in the
> coordinate file, there is no meaningful result. I understand I can use the
> -ur pbc mol command, but this just makes the molecule whole before bouncing
> across the screen. Any input would be helpful.
>

trjconv -pbc nojump

-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 629
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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