[gmx-users] Occupancy for a distance cut off

Justin Lemkul jalemkul at vt.edu
Tue Feb 12 02:19:12 CET 2013

On 2/11/13 6:15 PM, ram bio wrote:
> Dear Gromacs Users,
> I have a run a MD simulation on protein bound with ligand and ions
> using Gromacs 4.5.4. I am able to calculate the distances between ions
> and coordinating residues using g_dist. The output is in the form of
> xvg file, but I am looking for the occupancy for a cut off distance
> (3.5 Å) between ion and a particular residue atom during simulation.
> Please suggest.

g_dist -dist 0.35



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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