On Sat, 2012-05-05 at 13:19 +0200, Patrick Fuchs wrote: > >> Interesting discussion indeed. I'm just thinking that there might be > >> no fundamental difference to other thermostats. There's nothing in the > >> way that causes the friction, but then again, there's no physical > >> particle that causes the stochastic term in v-rescale, and the > >> Nosé-Hover particle is not physically "touching" the atoms either. In > >> all cases the surroundings couples to the atoms in a way that can't be > >> seen in e.g. a test tube. > >> > >> > >> Erik > >> > > > > Hi Erik, > > > > yes, that is a good point, which I haven't really thought about. > Indeed, in a macroscopic system heat will have to diffuse from the edges > of the container to the inside of the system. In the simulations, the > rescaling of velocities is done on all the atoms at the same time, > either on a local or global basis. For the use of SD in explicit > systems, the friction and stochastic terms (with the carefully chosen > friction coeffictient) can be seen as applying one thermostat per degree > of freedom. So Florian, I think you should change your view about the > random kicks and friction as a way to modify velocities for > thermostating, which is different from mimicking solvant effects in > implicit simulations (even if it uses also the friction and random > forces).
Yes, I know and already did so, as mentioned yesterday. > What we want is that the thermostat samples the proper > canonical ensemble. Then if it does, what also matters is to be aware > whether it affects other properties, notably dynamics (because rescaling > velocities will in general pertubs dynamics). There has been a nice > discussion some years ago in the GROMACS mailing list about that: > http://lists.gromacs.org/pipermail/gmx-users/2008-July/035302.html. Also > Bussi and Parrinello discuss this aspect in that paper: > http://dx.doi.org/10.1016/j.cpc.2008.01.006. Yes, I am aware of this, too, that is why a careful choice of the parameters is inevitable. Especially, the more you get into detail by reading various literature, the more you realize, that it is really not a simple task to sample an exact canonical ensemble. However, I thank you all again for this discussion, because thermostats and barostats are such an important topic. /Flo > Ciao, > > Patrick > > -- > _______________________________________________________________________ > Patrick FUCHS > Dynamique des Structures et Interactions des Macromolécules Biologiques > INTS, INSERM UMR-S665, Université Paris Diderot, > 6 rue Alexandre Cabanel, 75015 Paris > Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 > E-mail address: patrick.fu...@univ-paris-diderot.fr > Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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
