Re: [gmx-users] g_cluster Jarvis-Patrick

2010-07-14 Thread Ran Friedman 
Hi,

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.

Ran

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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[gmx-users] g_cluster Jarvis-Patrick

2010-07-13 Thread Marc Charendoff 
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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