[gmx-users] g_cluster cutoff

[Shay Teaching]

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 <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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