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

Berk Hess gmx3 at hotmail.com
Thu Jul 24 20:53:02 CEST 2008 

Hi,

Indeed, read the paper!

The stochastic term works on the "Berendsen scaling parameter" only.
It has the same correlation time as tau_t.
So the dynamics is nearly unaffected, surely less than with Nose-Hoover.

Berk.

> Date: Thu, 24 Jul 2008 17:26:00 +0200
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: Question about Berendsen thermostat	and	Nose-Hoover temp coupling (chris.neale at utoronto.ca)
> 
> 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.
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