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).
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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