[gmx-users] g_cluster cutoff
itamar.kass at monash.edu
Mon Sep 20 02:22:35 CEST 2010
I suggest you would look into the RMSD distribution inside your clusters
(file namermsd-dist.xvg). In this file you will see one or more peak.
The cut off you use should be larger then this peak but smaller then the
I know this is a bit simplicity, but for more you can search the mailing
On 20/09/10 9:12 AM, Shay Teaching wrote:
> I'm not sure this is necessarily the case. Have you tried other
> methods (gromos for example)? What are you getting when using other
> On Fri, Sep 17, 2010 at 6:14 PM, Kukol, Andreas <a.kukol at herts.ac.uk
> <mailto:a.kukol at herts.ac.uk>> wrote:
> 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
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"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
| Itamar Kass, Ph.D.
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