[AMBER] Clustering problem

From: Alessandro Mariani <alessandro.mariani.uniroma1.it>
Date: Wed, 17 Sep 2014 13:43:00 +0200

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.
I'm asking if there is a method, to identify a solute cluster using the
criterion of center of mass pair distance. If there is a ready-to-use tool
to do it, it will be great, but there will be no problem even if I'll have
to write it. I have some programming skills, I would say average, in C and
C++. In the attachments you will find a pseudo-program (no programming
language) that I was writing to solve this problem, but it has some
problems. The other file is a practical example of the program.


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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Received on Wed Sep 17 2014 - 05:00:03 PDT
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