[gmx-users] Berendsen Barostat for production runs

Mark Abraham mark.j.abraham at gmail.com
Thu Mar 28 13:44:18 CET 2019


I suggest you consider some of the seminal articles at
https://www.livecomsjournal.org/. They have articles discussing e.g.
foundational best practice for molecular simulations, and consider also
particular sub cases. I'm sure I read discussion of the topic in the last
few days, but forget in which article it was.


On Thu, 28 Mar 2019 at 13:17 Daniel Bauer <bauer at cbs.tu-darmstadt.de> wrote:

> Hi,
> I know that the usage of Berendsen baraostat for production runs is
> generally discouraged because it does not give a correct ensemble
> average. Nevertheless, I found some recent publications where this is
> done (presumably for performance reasons). Example: 10.1126/science.1254840
> What would be a justification that allows to do this? Under what
> conditions is it "ok" and when is it not? An explanation attempt by me
> is that Berendsen is fine if we do not try to investigate properties of
> the system that depend on the ensemble average (i.e ion conduction events).
> Best wishes,
> Daniel
> --
> Daniel Bauer, M.Sc.
> TU Darmstadt
> Computational Biology & Simulation
> Schnittspahnstr. 2
> 64287 Darmstadt
> bauer at bio.tu-darmstadt.de
> Don't trust atoms, they make up everything.
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