[gmx-users] a question about ensemble

[francesco oteri]

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!




> 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
>
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-- 
Cordiali saluti, Dr.Oteri Francesco
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