[gmx-users] params for g_cluster and g_clustsize

[David van der Spoel]

Dmitri Dubov wrote:
> 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?
Root mean square deviation. Typical for proteins.
> 
> 
> 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?

These are two different programs, unfortunately not sharing any code.
> 
> 
> Thanks.
> 
> 
> Dmitri
> 
> 
> 
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se