[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:
> 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?
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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