[gmx-users] g_cluster and g_clustsize confusion

David van der Spoel spoel at xray.bmc.uu.se
Sun Aug 23 22:15:48 CEST 2009

edmund lee wrote:
> Dear all, 
> When I am reading about the manual , I found that the g_cluster can 
> cluster structure with different type of methods, example, gromos, 
> monte-carlos and others.
> Then I also found that g_clustsize computes the size distribution 
> function of the molecules or atoms. (correct me if I am wrong)
> My questions are:
> Are these 2 programs (g_cluster and g_clustsize) related to each others?


> What does the method use in g_clustersize? Is it just depends on the 
> cut-off?

Yes. All atoms i that are within the cutoff distance from another atom j 
form a cluster together with atom j. This is mainly intended to analyze 
aggregation phenomena.

> Thanks.
> Yr comments and suggestions are appreciated.
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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

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