From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Mon Nov 20 2006 - 15:05:09 CST
If you have charmm/namd format trajectory files, CHARMM has a clustering
facility which can cluster any set of time series. If you cluster protein
dihedral angle time series, you will end up clustering conformations.
Look at the cluster command, and the correl command in correl.doc. There
must also be a discussion/thread in the charmm forum about this,
On Mon, 20 Nov 2006, L. Michel Espinoza-Fonseca wrote:
> 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 <davenky.namd_at_gmail.com>:
> > 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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