Re: clustering conformations

From: L. Michel Espinoza-Fonseca (
Date: Mon Nov 20 2006 - 14:49:16 CST


I think you'll find GROMACS useful to perform such task. Check out the
g_cluster utility:

I hope it helps.


2006/11/20, Dave Venky <>:
> Hi, I need to cluster 5000 snapshots from my simulations based on
> similar confomations. What is the best way to do this.
> I thought of calculating pairwise RMS deviations and cluster based
> on the RMS deivations. While I have calculated the RMS, I dont know how
> to cluster. Is there a program to do this?
> Thanks
> Dave

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