You would be best off using an RDF of particular atoms/functional groups to the waters. You can then integrate that and get the number of waters within a given distance.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of IISER_Minal Sent: Friday, 9 March 2012 3:46 PM To: [email protected] Subject: [gmx-users] Cluster analysis Hello, I would like to do cluster analysis in gromacs on my system which consists of a polymer and solvent . I would like to know how the solvent molecule surrounds around polymer and how many. Can anybody help me out that how to start with or use g_cluster or g_clustsize in gromacs. Also there are different methods available like linkage, jarvis-patrick, monte-carlo, diagonalization or gromos so which would be better to use. Thanx Minal More,
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