I'm not sure this is necessarily the case. Have you tried other methods (gromos for example)? What are you getting when using other methods? Regards, -Shay
On Fri, Sep 17, 2010 at 6:14 PM, Kukol, Andreas <[email protected]> wrote: > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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