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. > > > Erik >
Hi Erik, yes, that is a good point, which I haven't really thought about. Thanks, /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 > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > ----------------------------------------------- > 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 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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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