[gmx-users] a question about ensemble

Dommert Florian dommert at icp.uni-stuttgart.de
Fri May 4 10:45:58 CEST 2012

On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote: 
> Hi Florian,
> >> I remark that Langevin method is used also for explicit water system!
> >
> > But there a big question arises to me. The thermostatting by Langevin is
> > achieved due to random kicks. If I simulate all atoms explicitly, there
> > is only vacuum between the atoms. Where do the random kicks come from
> > and how do I set gamma, which is actually related to the viscosity of
> > the medium I am simulating in? If my medium is vacuum, then gamma should
> > be zero, shouldn't it, and gamma=0 means no coupling, and hence,
> > Newton's equation of motion are recovered.
> >
> > I am not an expert with the Langevin thermostat, so this are serious
> > questions that arise to me now. Furthermore I also thought, that
> > Langevin dynamics were exactly established for a description of a system
> > within a medium.
> The use of Langevin dynamics (SD) to mimic solvant implicitely or as a 
> thermostat in explicit systems depends on the friction coefficient you 
> choose. It has to be chosen with care, see for example 
> http://dx.doi.org/10.1007/b99427 or the GROMACS manual. In explicit 
> simulations, SD with the appropriate choice of friction coefficient can 
> be seen as a local thermostat. The advantage is that it samples the 
> canonical ensemble (in the old versions of GROMACS it was the only way 
> to get the canonical ensemble before the implementation of Nose-Hoover 
> or velocity rescaling).

Hi, thank you very much for pointing to this very interesting article.
However, though the method seems to work, gamma has a very big
influence. I also think, that this kind of coupling is not a good
picture for an explicit simulation, because there is nothing in space
where friction can arise from, so a reference how to obtain gamma is not

But thanks everybody of you for the nice discussion.


> 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
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