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

[Mark Abraham]

Hi,

Almost right. The behaviour of the Bussi v-rescale thermostat is equivalent
to Berendsen when the system is far from equilibrium, but has the right
distribution when it is in equilibrium (see discussion in Bussi's paper in
Diogo's first link). I know of no case where Berendsen works better than
v-rescale, so you may as well use it for both equilibration and production.
(Note that old literature referring to velocity-rescaling thermostats is
talking about something totally different.)

Mark

On Mon, Nov 28, 2016 at 11:26 AM Marlon Sidore <marlon.sidore at gmail.com>
wrote:

> 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.
> >
> --
> 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.