[gmx-users] a question about ensemble
francesco oteri
francesco.oteri at gmail.com
Thu May 3 11:31:05 CEST 2012
2012/5/3 Dommert Florian <dommert at icp.uni-stuttgart.de>
> 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.
>
>
Implicit Implicit solvent means accounting for the solvent presence without
including water atoms, look at
http://en.wikipedia.org/wiki/Implicit_solvation for details.
Regarding the collision source, it is water! The gamma value represent the
average collision frequence experienced by a protein atoms against water in
solution.
You have no water, so it models the water presence.
In implicit water simulation, usually a value close to 50 ps-1 (the
experimental values) is used, while for explicit water is used a value
around 2-5ps-1 bacause
water is present so it actually collides with protein.
> /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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--
Cordiali saluti, Dr.Oteri Francesco
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