From: pbrenne1_at_nd.edu
Date: Fri Jan 07 2005 - 15:58:41 CST

Hello,

Does anyone know if there is a built-in or plugin module for VMD to do cluster
analysis over a set of dcds? I have used VMD in the past to calculate RMSDs,
but currently I would like to perform conformational cluster analysis as
referenced by Smith, Daura, and Gunsteren in their 2002 Proteins paper. The
analysis is not difficult but a matrix (vector of vectors etc...) would be nice
to store the RMSD values in. From the VMD manual I understand that tcl is not
well suited for mathematical operations such as these. I have also noticed the
Cluster visualization plugin contributed by researchers at Cornell but my
initial review found that it required the actual computation be done via a
program written by the Sutcliffe Group in 1996 which does not appear to be open
source.

Thanks for any responses and my compliments on the VMD framework,
Paul Brenner