[gmx-users] a question about ensemble

Dommert Florian dommert at icp.uni-stuttgart.de
Thu May 3 10:40:49 CEST 2012

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


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.


> best
> Albert 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120503/0d277c0d/attachment.sig>

More information about the gromacs.org_gmx-users mailing list