[gmx-users] Cluster analysis

Dallas Warren Dallas.Warren at monash.edu
Mon Mar 12 02:08:57 CET 2012

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
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of IISER_Minal
Sent: Friday, 9 March 2012 3:46 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Cluster analysis


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.

Minal More,

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