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

ms devicerandom at gmail.com
Wed Aug 13 15:44:54 CEST 2014

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,

> Cheers,
> Tsjerk
> 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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