[gmx-users] Probability of number of atomic contacts

Justin Lemkul jalemkul at vt.edu
Sun Feb 17 13:39:28 CET 2019

On 2/17/19 7:21 AM, Mahsa wrote:
> Dear Gromacs users,
> I want to get histograms of the number of polymer-ion contacts average
> across the simulation. For this I used,
> gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od mindist.xvg
> -on numcont.xvg -or mindistres.xvg -group
> and from the index file, I chose the ion first and then the polymer group.
> The generated file numcont.xvg which is more related to what I am looking
> for, gives number of contacts vs time. How can I get the information which
> I look for from this analysis?

Post-process with gmx analyze -dist



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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