[gmx-users] Analyze neighbors of a residue within a cutoff distance during simulation

Justin Lemkul jalemkul at vt.edu
Tue Sep 1 13:32:08 CEST 2015

On 9/1/15 5:15 AM, Tushar Ranjan Moharana wrote:
> Hi Everyone,
> I have simulated a protein in 40 % methanol. Now I want to analyze the
> average distance between any amino acid and all the methanol molecule which
> comes to close to (less than 0.4 nm) that amino acid during the simulation.
> I tried many GROMACS analysis tool for this but I couldn't succeed. Can
> anybody kindly suggest me which analysis tool will be useful for me.

Use gmx select to generate index groups for each frame in the trajectory that 
identify methanol molecules that meet your criteria, then run gmx distance using 
those index groups (you need to do a per-frame analysis, e.g. loop the calls).



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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