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
> <https://networkx.github.io/documentation/latest/reference/generated/networkx.algorithms.components.connected.connected_components.html>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
convention.
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 03 2015 - 13:00:02 PDT
