Dear Marc: Please look towards g_clustzise (instead of g_cluster). We tried to use g_cluster some years ago and eventually switched to g_clustzise - I do not remember why but the latter was more successful. If you want to monitor the number of clusters in the system, g_clustzise can certainly do it.
Dr. Vitaly Chaban > I am trying to perform a cluster analysis on a 4 ns trajectory (4000 frame > trajectory), but I am not getting any more than 1 cluster until I get down to > a > cutoff of 0.05 nm. This seems like an awfully small number, so I checked my > rmsd > distribution and found that 44% of my rmsds are at 0.1 nm or greater. My > distribution looks like the following: > > And my command line is as follows: > > g_cluster -f md.trr -s md.tpr -n index.ndx -sz clustersize1.xvg -clid > clusterid1.xvg -cutoff .10 -cl clusters1.pdb -b 1 -e 4001 -- 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/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/mailing_lists/users.php
