Hi Tsjerk, sorry for the strong statement. I should have said:
should be applied ... instead of only applicable. You are right, the question is how big is the difference and actually one would also expect, that the differences vanish with 1/N. However, so far it is unknown, what kind of distributions Berendsen does produce and how this is related to the true canonical ensemble. For this reason, I would be very catious. In my studies I realized big differences in density and dynamical properties, if Berendsen instead of PR is used. Cheers, Flo On Wed, 2012-05-16 at 12:11 +0200, Tsjerk Wassenaar wrote: > Hi Florian, > > > Hi, there has been recently a discussion about this topic on this > > mailing list. Check the archives for the information you look for. > > However, Berendsen is not producing any kind of known ensemble, and > > therefore only applicable for equilibration. > > That's a very strong statement, and scientifically unsound. From a > theoretical statistical-mechanical perspective, the ensemble with the > Berendsen thermostat does not fall into the known classes. This > implies that using the Berendsen thermostat yields a physically > different ensemble. Yet the relevant question is whether the ensemble > is statistically significantly different, or even practically > significantly different. A next question is whether the difference > between two simulations with the Berendsen thermostat and two > simulations with one of the other ones is consistent or not. And when > comparing with experiments, are the predictions with the Berendsen > thermostat different from one of the others? > > This would be a very nice matter of debate if there was a difference > in performance using different thermostats. However (unfortunately? > ;)) there is not. So for the same cost there are thermostats that do > produce the desired ensemble, which makes these preferable over the > one from Berendsen (also for equilibration). That is not the same as > stating that it is only applicable for equilibration though. > > For the barostat it's a bit more complicated. Parrinello-Rahman can > not be used for equilibration, because a large deviation from the > target pressure may well cause large fluctuations that are unphysical > and may cause instability. So at the moment the Berendsen barostat > appears the only _one_ applicable for equilibration, but that doesn't > (yet) disqualify it for further use. > > Cheers, > > Tsjerk > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: [email protected] Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
signature.asc
Description: This is a digitally signed message part
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
