Subject: Re: CCL:Multiple Simulations

From: Anton Feenstra <feenstra(at)chem.vu.nl>
Date: Mon, 19 Jan 2004 12:23:42 +0100

Bimo Ario Tejo wrote:

> Dear Dr. Anton,
> 
> Have you received any respond from the list regarding your question? I have
> the same question with yours but until now I still have no idea how to solve
> it.

Not from the CCL, but I posted the same question on the Gromacs users list,
and got this answer from David L. Bostick:

Yes, there is a way to combine statistics from various simulations of the
same system.  Assuming, of course, that all systems are in equilibrium.
Assuming equilibrium, of course, allows us to avoid the problems
mentioned by Anton (homology models vs. x-ray structures ..etc.).

If the conditions (i.e. N,P, and T) are the same the average is linear.
However there are recently (~1990s) developed methods for overcoming
barriers for rare events in simulations by holding many simultaneous
simulations at different temperatures.  It was first designed for Monte
Carlo of glassy systems.  The data from these simulations can be combined
via multiple histogram methods.

The method is called Parallel Tempering and has been recently implemented
in MD simulation under the name of "Replica Exchange Molecular Dynamics."

A good description of the background can be found in:

Monte Carlo Methods in Statistical Physics by M.E.J. Newman and G.T.
Barkema (1999) Clarendon Press, Oxford.

And for the MD implementation,

Sugita, Y. and Okamoto, Y. Replica-exchange Molecular Dynamics Method for
Protein Folding. Chemical Physics Letters 314 (1999) 141-151.

-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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