[gmx-users] g_clustsize

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 12 15:48:40 CEST 2014

On 2014-06-12 15:33, Raisa Kociurzynski wrote:
> Dear Prof. Van der Spoel,
> I want to calculate the clustersize of GM1 clusters in a DPPC membrane. I used g_clustersize but when I use the option -mol the index file is ignored and the whole system is used for the calculation. Is there any way to specify only GM1 molecules for the cluster calculation? I also tried to modify my xtc and tpr files, so that my system consists only of GM1 molecules, but then I only get one big cluster with g_clustsize. I could not find any solution for this problem in the gromacs forum.
> Best regards,
> Raisa Kociurzynski
If you have a membrane there is only one cluster unless the membrane is 
fragmented into micelles.

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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