[gmx-users] How to calculate distance using gromacs?

Justin Lemkul jalemkul at vt.edu
Fri Feb 15 14:40:35 CET 2019

On 2/15/19 8:16 AM, Edjan Silva wrote:
> Dear,
> I performed a 100 ns simulation with B-DNA.
> I want to know which gromacs option I can calculate the distance between
> two DNA residues (guanine 5 and ADENIN 6, for example) during the 100 ns of
> simulation.

Create an index group for each base/nucleotide and use gmx distance:

gmx distance -s -f -select 'com of group "Gua5" plus com of group "Ade6"'

Substitute in whatever file names and group names are appropriate.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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