[gmx-users] trjconv options?

Justin Lemkul jalemkul at vt.edu
Wed Feb 3 13:37:54 CET 2016

On 2/3/16 6:34 AM, Timofey Tyugashev wrote:
> Thank you for replies on my previous questions.
> And now I have another one dealing with trjconv.
> I have a simulation of  a three-chain protein/nucleic acid complex. Naturally,
> it gets broken in three separate strands by PBC.
> After trying several, I settled on using options '-pbc mol' with '-ur compact'
> which makes the complex look decent again and it looks like that does the job.
> But I'm worried about a possibility of something getting unrepaired by this
> option and getting unnoticed by me. What is the way to check for it?

Any molecules that appear to fly away suddenly will be a pretty dead giveaway.

In general, for multimeric complexes, you need to do a lot more work, e.g. 
centering on a single chain after making molecules whole and removing jumps.  If 
a simple -pbc mol -ur compact does the trick, probably nothing has actually 
crossed a periodic boundary yet.

> Also it keeps tumbling around the cell during the trajectory. It's annoying. Is
> there a way to pin down the cluster and stop it from rotating?

This is what trjconv -fit is for.



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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