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 > -- > 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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