[gmx-users] a question about ensemble
dommert at icp.uni-stuttgart.de
Fri May 4 12:08:30 CEST 2012
On Fri, 2012-05-04 at 11:07 +0200, Erik Marklund wrote:
> 4 maj 2012 kl. 10.45 skrev Dommert Florian:
> > 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
> > given.
> > But thanks everybody of you for the nice discussion.
> > /Flo
> 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.
yes, that is a good point, which I haven't really thought about.
> > > 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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> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 6688 fax: +46 18 511 755
> erikm at xray.bmc.uu.se
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Dipl. - Phys.
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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