[gmx-users] a question about ensemble

Albert mailmd2011 at gmail.com
Thu May 3 10:45:32 CEST 2012

Hello Flo:

   thank you so much for your kind comments.
   Yes, I would like to couple the pressure, it really helps a lot.


On 05/03/2012 10:40 AM, Dommert Florian wrote:
> 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,
> 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
>> best
>> Albert
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