[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling (chris.neale at utoronto.ca)

[David van der Spoel]

Berk Hess wrote:
> 
> Hi,
> 
> 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 
meaningful then?

(I haven't read the paper of course :)).
> 
> Thanks for the tip!
> 
> Berk.
> 
> 
>  > 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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se