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

Michael Shirts michael.shirts at columbia.edu
Wed Jul 23 16:10:16 CEST 2008

> 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

Michael Shirts
Research Fellow
Columbia University
Department of Chemistry

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