[gmx-users] a question about ensemble
Dommert Florian
dommert at icp.uni-stuttgart.de
Thu May 3 11:22:04 CEST 2012
On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote:
> Hello,
>
> 2012/5/3 Dommert Florian <dommert at icp.uni-stuttgart.de>
> On Thu, 2012-05-03 at 07:32 +0200, Albert wrote:
> > hello:
> >
> > I wondering are the three thermostat methods: Langevin,
> Berendsen
> > and Nose-Hoover chain are all compatible with semi-isotropy
> coupling
> > style? If I would like to use semi-isotropy coupling method,
> which one
> > would be better?
> >
> > thank you very much
> >
>
> Hi,
>
> what should be coupled in a semi-isotropic manner ? I assume
> the
> pressure and now the question is, which thermostat to apply,
> isn't it?
>
> The three mentioned barostats are all of different kinds.
> While Langevin
> provides a thermostating method for implicit solvent, the
> other
> mentioned Thermostats are based on an explicit atom
> description of the
> system. However, the Berendsen thermostat quite old and not
> symplectic,
>
>
>
>
> I remark that Langevin method is used also for explicit water system!
But there a big question arises to me. The thermostatting by Langevin is
achieved due to random kicks. If I simulate all atoms explicitly, there
is only vacuum between the atoms. Where do the random kicks come from
and how do I set gamma, which is actually related to the viscosity of
the medium I am simulating in? If my medium is vacuum, then gamma should
be zero, shouldn't it, and gamma=0 means no coupling, and hence,
Newton's equation of motion are recovered.
I am not an expert with the Langevin thermostat, so this are serious
questions that arise to me now. Furthermore I also thought, that
Langevin dynamics were exactly established for a description of a system
within a medium.
/Flo
>
>
>
>
>
> which means that the phase space volume is not conserved.
> Fortunately,
> an updated method, the v-rescale thermostat of Bussi et al,
> has been
> published some years ago. It is quite similar to the Berendsen
> thermostat, but symplectic and suitable for production and
> equilibration. Finally the Nose-Hoover chain (NHC) is based on
> a
> extended Lagrangian for the system you want to simulate and
> corresponding equations of motions are applied in order to
> keep the
> temperature constant. NHC is symplectic, too, but not suitable
> for
> equilibration. However, as the only reasonable method for
> anisotropic
> pressure coupling is the Parrinello-Rahman (PR) barostat, or
> its
> extended version MTTK, which relies on the same idea as NHC, I
> would
> assume, that for production a combination of NHC and MTTK is a
> good
> choice. For the equilibration I would use a v-rescale
> thermostat and the
> Berendsen barostat, because PR and MTTK would take far too
> much time to
> achieve equilibrium.
>
> Hence, it much depends on the purpose, which combination of
> thermo- and
> barostat is the most suitable one.
>
> /Flo
>
>
>
> Anyway, I think that there is no strict coupling between temperature
> and pressure coupling:
> You need to keep the tempaerature fixed around a value and the same
> for pressure, so
> I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is,
> in priciple, right.
>
>
> Maybe convergence speed changes, but in this case banchmark are quite
> useful very welcolme!
>
>
> best,
> Francesco
>
>
>
> > best
> > Albert
> > --
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> --
> Florian Dommert
> Dipl. - Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> EMail: dommert at icp.uni-stuttgart.de
> Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>
> Tel.: +49 - (0)711 - 68563613
> Fax.: +49 - (0)711 - 68563658
>
> --
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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
> --
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--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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