[AMBER] Periodicity in MD simulations

From: Oliver Kuhn <oak.amber.googlemail.com>
Date: Mon, 18 Jul 2011 20:17:35 +0200

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 Mon Jul 18 2011 - 11:30:04 PDT
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