Re: [AMBER] algorithm for clustering solvent molecules?

From: Jason Swails <>
Date: Mon, 03 Aug 2015 15:31:21 -0400

On Mon, 2015-08-03 at 15:21 -0400, Jose Borreguero wrote:
> I have created a graph for every frame. Nodes in the graph are the solvent
> molecules, and two nodes are connected with and edge if the distance
> between the associated solvent molecules is below a cutoff I chose. I have
> systems with different solvation levels, some of then featuring "pockets"
> of solvent molecules. These pockets are the clusters I'm interested in.
> Algorithm networkx.connected_components
> <>can
> find the connected clusters from a graph. To create the graph, I am using
> MDAnalysis to obtain the contact map between solvent molecules. Regarding
> time, it takes 2.2seconds to create a contact map for 4132 solvent
> molecules, which I think is reasonable (unless you have many thousands of
> frames)

Neat idea! Even lets you account for PBC through the minimum image


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Aug 03 2015 - 13:00:02 PDT
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