[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca)
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 24 17:26:00 CEST 2008
Berk Hess wrote:
> That thermostat is really nice and also simple to implement.
> It is now in CVS.
If this thermostat has a stochastic term, is the dynamics still
(I haven't read the paper of course :)).
> Thanks for the tip!
> > Date: Wed, 23 Jul 2008 10:12:36 -0400
> > From: michael.shirts at columbia.edu
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Re: Question about Berendsen thermostat and
> Nose-Hoover temp coupling (chris.neale at utoronto.ca)
> > Note that a recently a velocity rescaling algorithm was developed in
> > the Parrinello group that does give the correct canonical ensemble.
> > See: http://arxiv.org/abs/0803.4060. It might be nice to replace
> > Berendsen with this algorithm, which should have the nice properties
> > of Berendsen (converges to the constraint temperature quickly) without
> > the serious drawbacks.
> > Cheers,
> > Michael
> > On Wed, Jul 23, 2008 at 10:10 AM, Michael Shirts
> > <michael.shirts at columbia.edu> wrote:
> > >> Have you seen any information to suggest that this is actually a
> > >> non-trivial concern? That is, given static point charges, an empirical
> > >> LJ force, short cutoffs, etc., do you believe that the application of
> > >> nose-hoover, berendsen, or even the arbitrary velocity rescaling
> > >> significantly degrades the quality of the obtained dynamics?
> > >
> > > 1) I think there's an important distinction to be made here between
> > > accuracy and physical validity. If you use a thermostat, then the
> > > dynamic properties you obtain for the system will be different than
> > > the properties obtained without the thermostat, independent of what
> > > model you choose. So, I don't know that it's that useful to ask
> > > whether the differences from the true system due to thermostat are
> > > large compared to the differences due to the choice of model -- the
> > > results are going to be dependent on the thermostat, so the field has
> > > chosen a standard definition of the dynamics, one that most resembles
> > > the actual physical system (where there isn't temperature rescaling
> > > every 2 fs or a piston coupled to a 10 nm cube of water, etc).
> > >
> > > 2) If one uses the Berendsen thermostat, then statistical mechanics of
> > > canonical ensembles will not strictly apply, and one can't use many of
> > > the results one would like to (or, are using already incorrectly).
> > > One can do physics-based simulation of molecular models, or one can do
> > > non-physics-based simulations of molecular models. In many cases, the
> > > non-physics-based results will be statistically indistinguishable from
> > > the physics based results. But why bother with an uncontrolled
> > > approximation when you don't -have- to use one? It just adds another
> > > chance that what one simulates is not reproducible or reliable, and
> > > heaven knows that simulation currently has enough of those already.
> > >
> > > It's like building a tower out of blocks, and each uncontrolled
> > > approximation, no matter how small, is a bit of unevenness in the
> > > block. If you have just one wobbly block, you can stand on it pretty
> > > well -- you know the limits of the approximation, you can get a pretty
> > > good sense of what's going on with the system. Once there's a large
> > > number of wobbly blocks, though -- good luck standing on top of it and
> > > trying to build good science. As simulations get larger and more
> > > complicated, they are built out of more and more blocks, and we need
> > > to make sure we're paying careful attention to how well they all fit
> > > together.
> > >
> > > Best,
> > > Michael Shirts
> > > Research Fellow
> > > Columbia University
> > > Department of Chemistry
> > >
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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