[gmx-users] The Berendsen thermostat does not generate the correct kinetic energy distribution.

[Marlon Sidore]

Berendsen does not generate the correct energy distribution but eliminates
fluctuations faster than v-rescale. That's why it is usually used during
equilibration.
You might want to switch to v-rescale for your production run (I'm not
sure, but the mdp files you got from charmm-gui probably already use
v-rescale for the production run).

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-11-28 11:17 GMT+01:00 Diogo Vila Viçosa <diogo.vicosa at fc.ul.pt>:

> I guess the best way to understand it is to read the original works:
>
> http://dx.doi.org/10.1063/1.448118
> http://dx.doi.org/10.1063/1.2408420
>
> And try to understand the differences between the two. Afterwards, you
> should be able to make a choice suitable for your case.
>
> Best,
> Diogo
>
> On Mon, Nov 28, 2016 at 4:48 AM Mijiddorj Batsaikhan <
> b.mijiddorj at gmail.com>
> wrote:
>
> > Dear gmx users,
> >
> > I want to simulation peptide on membrane. Initial structure was created
> by
> > Charmm-gui, and Charmm-gui gave appropriate mdp files. I have a question
> > about grompp's note.
> >
> > After energy minimization, I want to NVT equilibration, and grompp gave
> me
> > one note as a following
> >
> > ******
> >   The Berendsen thermostat does not generate the correct kinetic energy
> >   distribution. You might want to consider using the V-rescale
> thermostat.
> > ******
> >
> > How is V-rescale thermostat useful for the simulation?
> >
> >
> > Mijiddorj
> > --
> > 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 gmx-users-request at gromacs.org.
> >
> --
> 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 gmx-users-request at gromacs.org.
>