[gmx-users] a question about ensemble

Patrick Fuchs patrick.fuchs at univ-paris-diderot.fr
Sat May 5 13:19:43 CEST 2012

>> 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: 


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

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