[gmx-users] Berendsen Barostat for production runs

[Justin Lemkul]

On 3/28/19 8:44 AM, Mark Abraham wrote:
> Hi,
>
> 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.

https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0 
and references therein have good discussion on this topic.

-Justin

> Mark
>
> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
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