Re: [AMBER] Periodicity in MD simulations

From: Daniel Roe <>
Date: Tue, 19 Jul 2011 11:15:37 -0400


I assume you're talking about the "cluster" command in ptraj?

The "problem of periodicity" in clustering with the "sieve" keyword
can be illustrated with this simple example. Suppose you have a
trajectory in which you have a protein structure that has some sort of
periodic motion to it, let's say a domain motion which provides access
to an active site. For the purposes of this example lets say the
"open" conformation occurs about every 10 steps, and you choose to
cluster with a sieve of 10 - this means that on the first pass you are
effectively clustering based on a trajectory composed of entirely
"open" conformations, which is probably not desirable. However, if you
sieve randomly you are probably going to get a better representation
of the overall trajectory.

Clustering experts feel free to add to this or correct me but this is
how I understand "sieve" and periodicity.


On Mon, Jul 18, 2011 at 2:17 PM, Oliver Kuhn <> wrote:
> Dear Amber Users and Developers,
> I have read in the AmberTools Manual that the 'sieve' command can be set to
> What exactly is meant by that?
> I am asking because in the course of MMPBSA calculations I have done several
> 'independent' simulations using different intial random seeds.
> Sometimes simulations are totally uncorrelated, but sometimes they are all
> correlated together (for several nanoseconds). This can be seen in internal
> energies, e.g. angles (attached - 21 * 2ns simulation time HIV-Protease drug
> complex, blockwise averaged).
> I have read about synchronization effects of Langevin thermostat, but that
> is not what I observe. In my simulations I have the SAME starting structure
> and different seeds, not different structures and same seeds.
> I'm very puzzled about these correlations and have no idea what these are.
> What I know about the nature of correlations: Either simulations are
> correlated with pearson coefficient around 0.4 or uncorrelated with around
> 0.0 and nothing inbetween.
> My random seeds range from 01 02 and so on up to 21.
> Maybe someone can give me a hint for paper.
> Regards,
> Oliver
> --
> Oliver Kuhn, Department of Bioinformatics,
> Center for Medical Biotechnology, University of Duisburg-Essen,
> Universitätsstr. 1-5, 45141 Essen, Germany
> phone +49 201 183-3121,
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue Jul 19 2011 - 08:30:04 PDT
Custom Search