Re: [AMBER] algorithm for clustering solvent molecules?

From: Jason Swails <>
Date: Mon, 03 Aug 2015 13:17:09 -0400

On Mon, 2015-08-03 at 12:57 -0400, Jose Borreguero wrote:
> Thanks a lot, Jason. I'll go along with python for the clustering step. I
> found module networkx which is very straighforward for clustering, and
> quite fast.

How are you using networkx for this? I've used it to define a bond
graph in molecular topology before, but I don't see how networkx maps to
clustering here. Do you have a fully connected graph whose edge weights
are the distance between the nodes or something? That sounds like it
would be an expensive graph to create. Keep in mind that the PBC will
have an effect on the clusters, so how you pick the unit cell
representation is likely important.

I've used sklearn to cluster in the past, and I've found it to be pretty
easy to use, for what that's worth.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 03 2015 - 10:30:02 PDT
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