[gmx-users] g_clustsize and monomers

David van der Spoel spoel at xray.bmc.uu.se
Sun Mar 27 17:29:58 CEST 2011

On 2011-03-27 16.42, devicerandom wrote:
> Hi,
> I am trying to use g_clustsize to follow aggregation of peptides. I am
> currently using the following line:
> g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
> Problem is, it actually counts monomers as clusters. I have a system
> with 125 separate molecules, and the number of clusters starts from 125.
> What can I do to indicate a minimum cluster size?
> m.
What does it matter? Just simulate longer until you get two peptides to 
aggregate. Check eg. maxclust.xvg.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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