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 <scot...@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@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-requ...@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 -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
