[gmx-users] Multiple Simulations

David L. Bostick dbostick at physics.unc.edu
Mon Jan 12 17:11:01 CET 2004

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.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Mon, 12 Jan 2004, David van der Spoel wrote:

> On Mon, 12 Jan 2004, Anton Feenstra wrote:
> >Hi Users!
> >
> >
> >I've been looking through literature, but was unable to locate papers
> >that rigorously treat how to combine trajectories from multiple simulations
> >of the same system. In principle, one has to assign a (statistical)
> >weight to each of the simulations before taking, e.g., averages over
> >the combination. Can anyone give me a hint or a few pointers?
> Doesn't that depend on the kind of properties? If the simulations are
> under the same conditions (T,P etc.) then I'd say one can just
> linearly average most properties.
> >
> >
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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