Re: [AMBER] Temperature based trajectory in REMD

From: Daniel Roe <>
Date: Wed, 2 Oct 2013 11:22:15 -0600


On Wed, Oct 2, 2013 at 3:05 AM, Gargi Borgohai <> wrote:
> But at that temperature (i.e. 267
> K), I have carried out one set of conventional MD simulation (using the
> same force field viz. amber ff99SB) and the peptide did not show any sort
> of denaturation.

I would be wary of these results. How long are these simulations, and
what conformation did you start from? If it was the native state, it
may just be that your simulation is nowhere near converged and you are
just remaining near native because that's where you started. At 267 K
chances are your conformational search is slow, especially if you are
using explicit solvent.

> Will you please explain how many number of cluster should actually be
> assigned? What are the DBI and PSF values written in XXXout.txt file?

Clustering is really more of an art form because the parameters you
use depend on what clustering algorithm you are using and what your
distance matrix looks like (sparse, dense, etc). If you haven't
already, I recommend taking a look at:

J. Shao, S. W. Tanner, N. Thompson, T.E. Cheatham, III. "Clustering
molecular dynamics trajectories: I. Characterizing the performance of
different clustering algorithms." J. Chem. Theory Comp. 3, 2312-2334

The DBI stands for Davies-Bouldin index (essentially the average
similarity between a cluster and its closest counterpart), and PSF
stands for pseudo-F (the ratio of between-cluster variance to
in-cluster variance); these are both metrics which attempt to evaluate
how well your clustering has gone. You can look up the definitions for
them, but in general you want to minimize DBI and maximize PSF.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Oct 02 2013 - 10:30:04 PDT
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