[gmx-users] a question about ensemble
dommert at icp.uni-stuttgart.de
Thu May 3 10:50:19 CEST 2012
On Thu, 2012-05-03 at 10:45 +0200, Albert wrote:
> Hello Flo:
> thank you so much for your kind comments.
> Yes, I would like to couple the pressure, it really helps a lot.
You're welcome. There is just one little typo
> 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
it means thermostats and not barostats
> > 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
> > > --
> > > 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
> gmx-users mailing list gmx-users at gromacs.org
> 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
Dipl. - Phys.
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
-------------- next part --------------
A non-text attachment was scrubbed...
Size: 198 bytes
Desc: This is a digitally signed message part
More information about the gromacs.org_gmx-users