[gmx-users] Measuring distances between residues and visualising the results

Justin Lemkul jalemkul at vt.edu
Tue Aug 19 18:53:35 CEST 2014

On 8/19/14, 11:03 AM, Nikolaos Michelarakis wrote:
> Hello,
> I am trying to measure the distances between certain residues over the
> course of my simulation. I have created an index with these residues. So
> far i have tried using gmx mdmat but since there are only five residues the
> resulting map consists of 25 large boxes, of different shades, which is not
> very useful. I have also tried using gmx distance but I am not sure if I am
> using it correctly. When it prompts me to select the groups do I choose the
> index group twice?

If you do that, you'll just get zeroes - the distance between a group an itself.

> Any suggestions on how to better visualize the gmx_mdmat results or use gmx
> distance accurately?

See gmx distance syntax and usage here:




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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