[gmx-users] Questions about Thermostats

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 16 12:11:56 CEST 2012

Hi Florian,

> Hi, there has been recently a discussion about this topic on this
> mailing list. Check the archives for the information you look for.
> However, Berendsen is not producing any kind of known ensemble, and
> therefore only applicable for equilibration.

That's a very strong statement, and scientifically unsound. From a
theoretical statistical-mechanical perspective, the ensemble with the
Berendsen thermostat does not fall into the known classes. This
implies that using the Berendsen thermostat yields a physically
different ensemble. Yet the relevant question is whether the ensemble
is statistically significantly different, or even practically
significantly different. A next question is whether the difference
between two simulations with the Berendsen thermostat and two
simulations with one of the other ones is consistent or not. And when
comparing with experiments, are the predictions with the Berendsen
thermostat different from one of the others?

This would be a very nice matter of debate if there was a difference
in performance using different thermostats. However (unfortunately?
;)) there is not. So for the same cost there are thermostats that do
produce the desired ensemble, which makes these preferable over the
one from Berendsen (also for equilibration). That is not the same as
stating that it is only applicable for equilibration though.

For the barostat it's a bit more complicated. Parrinello-Rahman can
not be used for equilibration, because a large deviation from the
target pressure may well cause large fluctuations that are unphysical
and may cause instability. So at the moment the Berendsen barostat
appears the only _one_ applicable for equilibration, but that doesn't
(yet) disqualify it for further use.



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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