Hi Tsjerk,
On 8/13/14 3:19 PM, Tsjerk Wassenaar wrote:
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.
I am sorry, but I don't understand anything here - what does
"within-cluster RMSD" means? what is the "between-clusters RMSD"?
I would expect the RMSD distribution to mirror the RMSD vs time plot ;
that is, if I take the points from the rmsd-time.xvg and I make an
histogram, I would expect to recover the RMSD distribution. Am I wrong?
thanks a lot for your help,
m.
Cheers,
Tsjerk
On Wed, Aug 13, 2014 at 3:14 PM, ms <deviceran...@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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