[gmx-users] Berendsen Barostat for production runs
jalemkul at vt.edu
Thu Mar 28 13:47:34 CET 2019
On 3/28/19 8:44 AM, Mark Abraham wrote:
> 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.
and references therein have good discussion on this topic.
> On Thu, 28 Mar 2019 at 13:17 Daniel Bauer <bauer at cbs.tu-darmstadt.de> wrote:
>> 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 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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Justin A. Lemkul, Ph.D.
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