[gmx-users] Interatomic distance matrices

[Tsjerk Wassenaar]

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...

Cheers,

Tsjerk

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
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-- 
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