VMD-L Mailing List

From: lug2002_at_med.cornell.edu
Date: Fri Jan 07 2005 - 23:41:14 CST

Hi Paul,

I wrote the cluster plugin for vmd. You are right, it uses nmrcluster to
do the actual calculation. The plugin then parses the output to do the
visualization. This parsing subroutine is independent of the rest of the
program and other subroutines could be easily programed to parse the
output of other clustering programs. Where you thinking of any in
particular?
Regards,
Luis Gracia

> 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
>
>
>