[gmx-users] params for g_cluster and g_clustsize

Dmitri Dubov ddubov at ngs.ru
Sun Jul 5 14:06:07 CEST 2009

Dear gmx'ers,

Could you explain me the following points in manuals for g_cluster and g_clustsize programs?

1) Manual for g_cluster:
"single linkage: add a structure to a cluster when its distance to any element of the cluster is less than cutoff...
Other options...
-cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor"
What does "RMSD" mean here?

2) Manual for g_clustsize:
"-cut real 0.35 Largest distance (nm) to be considered in a cluster"
Is there any difference between -cut and -cutoff in g_cluster above?


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