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.
Mark On Thu, 28 Mar 2019 at 13:17 Daniel Bauer <[email protected]> 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 > [email protected] > > Don't trust atoms, they make up everything. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
