[gmx-users] a question about ensemble
patrick.fuchs at univ-paris-diderot.fr
Thu May 3 18:43:08 CEST 2012
>> 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).
Dynamique des Structures et Interactions des Macromolécules Biologiques
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