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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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