[gmx-users] a question about ensemble

Dommert Florian dommert at icp.uni-stuttgart.de
Thu May 3 12:12:31 CEST 2012


On Thu, 2012-05-03 at 11:31 +0200, francesco oteri wrote:
> 
> 
> 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

And why do I simulate explicit water, if I have already included water
in the collision term ? My question arose because you have written, that
Langevin is also applied in explicit water simulations. Now you are only
talking about implicit solvent simulations. For this purpose Langevin is
surely fine, because it has especially develop for such a situation.

/Flo


> 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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-- 
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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