[gmx-users] defination of cluster

[Q. Y. HUAN]

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?

Thanks for any comments.

QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.