Re: [AMBER] Periodicity in MD simulations

From: Ignacio J. General <>
Date: Tue, 19 Jul 2011 11:09:17 -0400

Dear Oliver,

I am not sure if I would say that you have a problem of periodicity.
To make my point, let me make a huge simplification to your case.
Let's say that your system consists of a spring, whose energy has been
minimized; in other words, it is in its equilibrium length. If you now
apply a force to it, it will start to oscillate with a given period.
But if you now go back to the minimized spring and apply a different
force, it will again start to oscillate with the same period! That is,
of course, because the period is a function of the spring constant and
its mass, not of the force (or initial velocity) you apply.

So, if you start with the same minimized structure, I think I would
expect a potential energy plot like the one you attached, with
approximately the same frequencies but different amplitudes. In order
not to see that, you should start with different initial structures,
in which case the frequency will still be the same, but the plots of
each case will be displaced, so they won't appear correlated.


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,
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Received on Tue Jul 19 2011 - 08:30:04 PDT
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