[gmx-users] defination of cluster

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 28 02:24:52 CET 2008

Q. Y. HUAN wrote:
> Dear all, 
> I did the g_clustsize to get the number of cluster graph for my system. At the end of the simulation, the total number of cluster shown in the graph of my system was 8. Then I had a view in the trjectory and I found that there were total of 8 aggregated micelles and some free monomer (even it is a single molecule) which is same with the result shown in the graph.
> ie 8 in the graph, 8 in the trajectory
> My question is, how Gromacs define the defination of cluster? In my case, is it a free monomer (single free molecule) is also counted?

Did you start by reading g_clustsize -h?


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