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?
8 aggregated micelles, 8 clusters detected...sounds to me like the micelle is
the cluster, not the monomer. From g_clustsize -h, read the description of the
-cut option.
-Justin
Thanks for any comments.
QIU YI HUAN
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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