[gmx-users] centering molecule for movies

Justin Lemkul jalemkul at vt.edu
Mon Jul 7 18:48:24 CEST 2014

On 7/7/14, 8:42 AM, Neha Gandhi wrote:
> Hi List,
> I have simulated peptides in explicit water to form aggregate. I tried
> various options to post-process my trajectory (after removing water) using
> Gromacs 4.6.3 as described below. I want to record movie using VMD but the
> molecule translates and rotates during movie hence, I cannot capture all
> screen shots properly.
> trjconv -f md.xtc -pbc mol -o x.xtc -s md.tpr -n index.ndx
> trjconv -f x.xtc -ur compact -center -s md.tpr -n index.ndx
> How do I keep the peptides in center to record the movie? Is it a vmd
> problem or post-processing issue will fix it? If anybody has faced similar
> issue and has found a solution, i would appreciate your help.

Dealing with multiple peptides is like herding cats.  The easiest approach is to 
focus on one peptide, i.e. one that forms some convenient reference point (maybe 
it becomes somewhat centered in the aggregate), and do translational and 
rotational fitting on it.  The others will fly around it for a while, but if 
they aggregated, they will all eventually converge around the position of the 
fitted peptide.



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


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