[gmx-users] defination of cluster

[Justin A. Lemkul]

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.
> 
> 
>       
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
========================================

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

========================================