[gmx-users] g_cluster cutoff

Shay Teaching shay.teaching at gmail.com
Mon Sep 20 01:12:49 CEST 2010

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?

On Fri, Sep 17, 2010 at 6:14 PM, Kukol, Andreas <a.kukol at herts.ac.uk> 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
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