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 -- 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