it's not really clear what you are asking.
On Mon, Jul 18, 2011 at 2:17 PM, Oliver Kuhn <oak.amber.googlemail.com>wrote:
> Dear Amber Users and Developers,
>
> I have read in the AmberTools Manual that the 'sieve' command can be set to
> random to avoid THE POTENTIAL PROBLEM OF PERIODICITY.
> 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, oliver.kuhn.uni-due.de
>
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Received on Tue Jul 19 2011 - 08:00:03 PDT
