[gmx-users] g_mindist works along trajectory? (gromacs 4.6)

Justin Lemkul jalemkul at vt.edu
Wed Aug 27 20:14:45 CEST 2014

On 8/27/14, 2:10 PM, ms wrote:
> Dear Gromacs users,
> I am using Gromacs 4.6. I would like to plot the contacts (minimum atom-atom
> distances) between some residue side chains and a ligand along a trajectory. I
> thought I would find the solution in g_dist or g_mindist, however, if I
> understand correctly:
> - g_dist calculates the distances between the *center of mass* of a group (say,
> the residue) and another (say, the ligand). This is not really what I want,
> since I want the *minimum* distance between the two groups, to declare it a
> contact or not.
> - g_mindist calculates the minimum distance between the two groups ; however it
> seems to me it does give the minimum distance along *all* the trajectory, not
> for each individual frame. Am I wrong?

g_mindist will plot the minimum distance of any atom pairs frame by frame.

> In short, what's the best strategy to accomplish what I am trying to do?

g_mindist should handle all of this.



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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