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

[Mijiddorj Batsaikhan]

Thank you all.

I used v-rescale thermostat as following options for NVT and NPT
equilibration. From the manual, v-rescale needs to set the random seed with
*ld-seed*. This thermostat works correctly even for *tau-t = 0*.
Are the following options correct?

*For NVT:*
tcoupl = v-rescale
tc_grps = PROT MEMB SOL_ION
tau_t = 0 0 0
ref_t = 298 298 298
ld-seed = -1


*For NPT:*

tcoupl = v-rescale
tc_grps = PROT MEMB SOL_ION
tau_t = 1.0 1.0 1.0
ref_t = 298 298 298
ld-seed = -1

Best regards,

Mijiddorj


> ------------------------------
>
> Message: 5
> Date: Mon, 28 Nov 2016 13:20:13 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] The Berendsen thermostat does not generate
>         the correct kinetic energy distribution.
> Message-ID:
>         <CAMNuMARVp5WPou6aMi0QUt-uhYn8JSdYeE-iHk8=cy1T9t45bQ@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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'Ing?nierie des Syst?mes Macromol?culaire (LISM)
> > CNRS - UMR7255
> > 31, Chemin Joseph Aiguier
> > 13402 cedex 20 Marseille
> > France
> >
> >
> > 2016-11-28 11:17 GMT+01:00 Diogo Vila Vi?osa <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
> > > > --
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