[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 15:14:41 CEST 2014

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 

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?


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