[gmx-users] Pressure coupling in expanded ensemble simulations

[Michael Shirts]

Ah, sorry, I thought there was more information coming.

Have you considered just using temperature replica exchange?  It's not that
much less efficient, and is easier to deal with.  Replica exchange should
be working with NPT (as long as you use Parrinello-Rahman and a reasonable
temperature control algorithm).  The size scaling is about the same; i.e.
if you need a lot of replicas, you will also need a lot of expanded
ensemble intermediates.




On Fri, May 17, 2019 at 8:06 AM Gregory Man Kai Poon <gpoon at gsu.edu> wrote:

> Hi Michael,
>
> I am just following up on your thoughts on how carrying out expanded
> ensemble at NVT and converting back to NPT on the mailing list.  Again I
> appreciate your advice in this area.
>
> Best wishes,
>
> Gregory
>
>
> On 5/8/2019 12:01 PM, Michael Shirts wrote:
>
> Yeah, this is an unfortunately place in the code where not all combinations
> work - very long story.  Hopefully this will be working better in 2020.
>
> What I would recommend is, if possible, performing the expanded ensemble
> simulation at NVT.  Everything should work fine there (paper coming out
> hopefully soon comparing a bunch of free energy methods).  Once can always
> correct the free energy at lambda=1 from NVT to NPT.  I Can fill in the
> details.
>
> You do NOT want to do Berendsen for NPT when running expanded ensemble.
> The results will be incorrect (as I have learned by sad experience_
>
> On Wed, May 8, 2019 at 8:14 AM Gregory Man Kai Poon <gpoon at gsu.edu
> ><mailto:gpoon at gsu.edu> wrote:
>
>
>
> Hi all:
>
> We are interested to do expanded ensemble simulations (such as simulated
> tempering) on GROMACS.  Extensive fiddling with the settings and
> googling on other people's experience suggests that these simulations
> must use the md-vv integrator, which in turn is compatible with
> Berendsen or MTTK coupling for pressure.  However, MTTK does not work
> with constraints, which are needed for the forcefields.  Berendsen can
> handle constraints but is not recommended for preserving thermodynamic
> ensembles.  Any ideas on how one should proceed?
>
> Many thanks for your thoughts.
>
> Gregory
>
>
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> --
>
> Gregory M. K. Poon, PhD, RPh
> Associate Professor
> Departments of Chemistry and Nutrition | Georgia State University
> NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
> P.O. Box 3965 | Atlanta, GA 30303
> Ph (404) 413-5491 | gpoon at gsu.edu<mailto:gpoon at gsu.edu>
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