[gmx-users] g_cluster analysis

SAPNA BORAH sapnauser365 at gmail.com
Mon May 23 09:03:37 CEST 2016

Dear all,

I am trying to use g_cluster protocol to get representative snapshots of
the simulations. I have concatenated 9 set of simulations and run g_cluster
for the same. The result shows a total of 198 clusters.

Is this correct?

Following is the command I have used:

g_cluster -s models.gro -f concatenated.xtc -dm rmsd-matrix.xpm -o
clusters.xpm -sz cluster_size.xvg -clid cluster-id-over-time.xvg -cl
all_clusters.pdb -cutoff 0.2 -method gromos

Thanks in advance.


Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,

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