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. > > best > Albert >
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 /Flo > > 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@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-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > gmx-users mailing list gmx-users@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-requ...@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: domm...@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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