[gmx-users] Interatomic distance matrices

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Feb 23 20:27:15 CET 2011

Hi Nathan,

g_rmsdist gives full matrices, and in .xpm format for which you'd need
to do more scripting than for your original problem :)
But you might find genrestr useful. It can generate constraints for
all distances in a selection, which means you get a half matrix with
the distances. They're not going to be formatted as a half matrix
though. Maybe take these 15 minutes to script it...



On Wed, Feb 23, 2011 at 7:47 PM, J. Nathan Scott
<scottjn at chemistry.montana.edu> wrote:
> 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,
> Nathan
> --
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list