[gmx-users] Centring a protein complex

Justin Lemkul jalemkul at vt.edu
Wed Oct 29 14:23:40 CET 2014

On 10/29/14 8:56 AM, Rohit Farmer wrote:
> Hi Justin,
> Thanks for the advice. It was the problem with the .xtc file I was using it
> worked when I used the .trr file I think something went wrong while
> downloading the files from our computer cluster.
> One more qustion I have. My molecule looks broken at several places. I know
> that it is just an artefact and not that its actually broken. But is there
> a way to make then look whole. I tried the option whole with -pbc but
> couldn't figure out what it actually did.

Using -pbc whole or -pbc mol should do the job.  Proper representation of 
everything (making things whole, removing jumps, fitting, etc) usually takes 
several passes through trjconv.



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


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