[gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 13 15:19:17 CEST 2014

Hi Massimo,

You have two clusters, both with low within-cluster RMSD. This shows up as
the first peak in the RMSD distribution. The second peak is the
between-clusters RMSD.



On Wed, Aug 13, 2014 at 3:14 PM, ms <devicerandom at gmail.com> wrote:

> Dear Gromacs users,
> I am analyzing the RMSD evolution of a trajectory with g_rms and
> clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing something
> quite odd in the RMSD distribution. I link here the RMSD evolution over
> time , the cluster ID over time, and the RMSD distribution (see
> http://imgur.com/a/0ftA2 ).
> RMSD evolution in time and cluster ID in time seem to make sense -the
> larger cluster is cluster 1, and it indeed populates most of the trajectory.
> The RMSD distribution is also correctly bimodal and peaked around the
> right values, at least visually. However, I would expect that the peak
> around 0.3-0.4 should be larger than the peak around 0.1, given the time
> evolution/distribution of RMSD, yet I see the opposite, apparently. What
> does it mean?
> Thanks,
> Massimo
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Tsjerk A. Wassenaar, Ph.D.

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