From: Axel Kohlmeyer (
Date: Wed Sep 17 2014 - 04:41:59 CDT

On Wed, Sep 17, 2014 at 4:57 AM, Alessandro Mariani
<> wrote:
> 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?

this is the kind of inquiry that is almost impossible to answer in a
helpful manner.
what is it that you are asking for? and what is the kind of effort
that you are willing to invest? and what is the level of your
programming skills (in general, and in VMD/Tcl)?

there are plenty of papers and instructions for the individual steps available.

> 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
> _____________________________________________

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.