VMD-L Mailing List

From: Alessandro Mariani (alessandro.mariani_at_uniroma1.it)
Date: Wed Sep 17 2014 - 03:57:10 CDT

Hello,
I'm currently having some problems and maybe you can help me.
I have a MD trajectory (Amber xtc) where are visible some solute clusters.
The thing I want to do is to identify these clusters (i. e. which molecules
are part of it) and then compute the lifetime of them (as an
autocorrelation function). The criterion of two molecules to be in the same
cluster is that their centre of mass are within a certain distance.

Any idea?

Thanks for help
_____________________________________________

Dr. Alessandro Mariani

PhD Student
Department of Chemistry
"La Sapienza" University of Rome
P.le Aldo Moro, 5
00185 Rome (IT)

Telephone: +39 06 49934082
Mobile Phone: +39 340 4124911
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