Hi, I am using g_cluster to analyse a trajectory (protein backbone):
g_cluster -f traj.xtc -s topol.tpr -g cluster.log -skip 10 -cutoff 0.5 -fit -method linkage As a result I get almost hundred clusters. The plot of the RMSD against time for the same trajectory generated with g_rms shows a maximum RMSD just below 0.5 nm. Therefore, with a -cutoff of 0.5 nm, I would expect to find that the whole trajectory clusters into ONE cluster. Am I expecting something wrong or is there a problem with g_cluster ? (using Gromacs 4.07) Many thanks Andreas -- 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
