[gmx-users] Re: g_cluster settings

Vitaly Chaban vvchaban at gmail.com
Mon Jul 12 07:11:21 CEST 2010

Dear Marc:

Please look towards g_clustzise (instead of g_cluster). We tried to
use g_cluster some years ago and eventually switched to g_clustzise -
I do not remember why but the latter was more successful. If you want
to monitor the number of clusters in the system, g_clustzise can
certainly do it.

Dr. Vitaly Chaban

>     I am trying to perform a cluster analysis on a 4 ns trajectory (4000 frame
> trajectory), but I am not getting any more than 1 cluster until I get down to a
> cutoff of 0.05 nm. This seems like an awfully small number, so I checked my rmsd
> distribution and found that 44% of my rmsds are at 0.1 nm or greater. My
> distribution looks like the following:
> And my command line is as follows:
> g_cluster -f md.trr -s md.tpr -n index.ndx -sz clustersize1.xvg -clid
> clusterid1.xvg -cutoff .10   -cl clusters1.pdb -b 1 -e 4001

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