Shalom Andreas,
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
second peak.
I know this is a bit simplicity, but for more you can search the mailing
list.
Cheers,
Itamar
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
methods?
Regards,
-Shay
On Fri, Sep 17, 2010 at 6:14 PM, Kukol, Andreas <a.ku...@herts.ac.uk
<mailto:a.ku...@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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"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.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
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