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). 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.
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
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