On Tue, 2012-05-15 at 19:47 +0100, Lara Bunte wrote: > Hello > > To make better energy minimization procedures I read about thermostats and > barostats. I understand the physical concepts and differences between global > and local thermostats and the difference between Berendsen and Nose-Hoover > thermostat. > > 1.) > Maybe this question is a little bit hairsplitting, but: This concepts of > thermostats and barostats, is this Thermodynamics, is this Kinetics, is this > statistical physics? What is it if I want to give this a name. > > 2.) > I read, that local thermostats, i.e. stochastic dynamics produce a NVT > ensemble, which is a canonical ensemble and that this alway fulfills > Ergodicity Theorem. About this I have following question: In my literature > they said, that this means, that all degrees of freedom in the system are > coupled strong enough each other. This confuses me. I learned, that > ergodicity means, that the complete phase space is passed by a trajectory, if > we wait long enough. This means, that ensemble average is equal to time > average of the system. Where is in my statement about ergodicity the meaning > of "all degrees of freedom in the system are coupled strong enough" Do this > in fact mean, that the complete phase space is passed? > > 3.) > I ask myself what I should use. First question: Local or global thermostat? I > guess (not knowing, guessing), that global is better for energy minimization, > because as far as I understand, it is more stable than local description. > From a physical point of view I think Nose-Hoover shoul be always better, > because it produces a real canonical ensemble, while Berendsen is > microcanonical ensemble, which is totaly unrealistic?! In an microcanonical > ensemble, energy is not changed with the enviroment. This makes no sense? > > Thanks for helping me > Greetings > Lara >
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. /Flo -- 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
signature.asc
Description: This is a digitally signed message part
-- 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
