[gmx-users] g_cluster Jarvis-Patrick

Ran Friedman r.friedman at bioc.uzh.ch
Wed Jul 14 09:54:59 CEST 2010


The nearest neighbours are defined according to RMSD between the
structures. If M=10, a new conformation x is added to a given cluster
when a conformation y in the cluster exists such that:
(1) x and y are neighbours, i.e., x has y among the 10 conformations
with minimal RMSD to x and vice versa for y.
(2) x any y have at least P (default: 3) neighbours in common.

You may want to prepare a diagram to graphically illustrate this.


Marc Charendoff wrote:
> Hello,
>      In the Jarvis-Patrick method g_cluster shows that when M=0, the
> cutoff is used to determine nearest neighbors (those within X.X nm).
> In the absence of cutoff - e.g. M is defaulted to 10, how are nearest
> neighbors determined? What does M=10 (or anyother number) mean?
> Thanks, Marc

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