[gmx-developers] More about the Ekin issue.

David spoel at xray.bmc.uu.se
Thu Aug 11 19:01:06 CEST 2005

> > The acceptance ratio does not say anything about efficiency.
> > The pV term is roughly 10x larger the energy term, so the energy 
> > difference
> > has a negligible influence on the exchange probability.
> > The exchange probability is almost fully determined by pV.
> > Fluctuations in the solvent probably contribute most to pV.
> > So you just exchange based on fluctuations in the solvent
> > and not on the conformation of the solute.
> > I have no idea how efficient REMD based (mainly) on the pV criterion is.
> >
> > Another issue is that the pV distribution with Berendsen pressure
> > coupling is quite off for small systems. For 400 waters:
> > Berendsen: pV RMSD 375 kJ/mol
> > Parrinello-Rahman: pV RMSD 490 kJ/mol
> >
> Now I thought a bit more I think the huge fluctuations are the problem.
> The average pV for 400 waters should be around 12 kJ/mol.
Where do you get that number from?

There definitely is no detectable correlation between protein structure
and energy...

> If there were no large fluctuations the exchange criterion would produce
> proper and efficient REMD sampling. An increased temperature might
> increase the average pV by 0.1 kJ/mol.
> But the enourmous fluctuations will dominate the exchanges and cause
> all exchanges to be random. If you attempt to exchange infrequently
> the normal MD sampling will correct a bit for this, but the ensembles
> will probably still be quite incorrect.
> (Note that a molecular virial will not help as there are no intramolecular
> interactions in water)
> Berk.
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David van der Spoel, PhD, Assoc. 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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