[gmx-users] a question about ensemble

Dommert Florian 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 
> 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.


> 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.fuchs at 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: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120505/403b451e/attachment.sig>

More information about the gromacs.org_gmx-users mailing list