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 > 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@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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