[gmx-users] Interatomic distance matrices

J. Nathan Scott scottjn at chemistry.montana.edu
Wed Feb 23 19:47:07 CET 2011

Dear Gromacs users,

I was wondering, is there any utility in Gromacs for calculating and
saving a triangular matrix of interatomic distances from a trajectory
frame? The website mailing list search seems to be down, and Google
has not been of much help. g_rmsdist looks like it *might* be able to
do this, but from the documentation I can't tell whether or not there
is a set of switches that would allow one to turn off the
averaging/rms calculation features and instead generate a single frame
static distance matrix.

If Gromacs can't do this, can anyone recommend another program that
could generate such matrices? This would not be hard to code, but time
savers are always appreciated. :)

Best Wishes,

J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University

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