[gmx-users] a question about ensemble
dommert at icp.uni-stuttgart.de
Sat May 5 13:44:10 CEST 2012
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
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:
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.
> 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.fuchs at univ-paris-diderot.fr
> Web Site: http://www.dsimb.inserm.fr/~fuchs
Dipl. - Phys.
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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