2012/5/3 Dommert Florian <domm...@icp.uni-stuttgart.de> > On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: > > Hello, > > > > 2012/5/3 Dommert Florian <domm...@icp.uni-stuttgart.de> > > 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, > > > > > > > > > > I remark that Langevin method is used also for explicit water system! > > But there a big question arises to me. The thermostatting by Langevin is > achieved due to random kicks. If I simulate all atoms explicitly, there > is only vacuum between the atoms. Where do the random kicks come from > and how do I set gamma, which is actually related to the viscosity of > the medium I am simulating in? If my medium is vacuum, then gamma should > be zero, shouldn't it, and gamma=0 means no coupling, and hence, > Newton's equation of motion are recovered. > > I am not an expert with the Langevin thermostat, so this are serious > questions that arise to me now. Furthermore I also thought, that > Langevin dynamics were exactly established for a description of a system > within a medium. > > Implicit Implicit solvent means accounting for the solvent presence without including water atoms, look at http://en.wikipedia.org/wiki/Implicit_solvation for details.
Regarding the collision source, it is water! The gamma value represent the average collision frequence experienced by a protein atoms against water in solution. You have no water, so it models the water presence. In implicit water simulation, usually a value close to 50 ps-1 (the experimental values) is used, while for explicit water is used a value around 2-5ps-1 bacause water is present so it actually collides with protein. > /Flo > > > > > > > > > > > > > > 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 > > > > > > > > Anyway, I think that there is no strict coupling between temperature > > and pressure coupling: > > You need to keep the tempaerature fixed around a value and the same > > for pressure, so > > I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, > > in priciple, right. > > > > > > Maybe convergence speed changes, but in this case banchmark are quite > > useful very welcolme! > > > > > > best, > > Francesco > > > > > > > > > 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 > > > > -- > > 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 > > > > > > > > > > -- > > Cordiali saluti, Dr.Oteri Francesco > > -- > > 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 > > -- > 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 > -- Cordiali saluti, Dr.Oteri Francesco
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