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Hi,<br><br>Strictly speaking you should never have thermostats for separate parts<br>of the system when those parts are coupled through potentials.<br>But in practice you can have integration errors which heat or cool different<br>parts of the system in different ways.<br>I think that for most systems only the electrostatics treatment will have<br>a significant effect. Plain Coulomb cut-off and reaction-field both produce<br>large integration errors. With PME you should never need multiple t-coupl groups.<br><br>The other issue is slow heat exchange between different parts of the system.<br>For a protein in solvent I think this is never an issue. But for other systems<br>it could be. Here it is the question if your simulation is much longer<br>than this exchange time or not.<br>The Berendsen thermostat can produce artifacts when you have weakly<br>coupled modes. but with Gromacs 4 there is no reason to use Berendsen,<br>since we have v-rescale and Nose-Hoover.<br><br>I think you can always use PME, v-rescale or nose-hoover and a single<br>t-coupling group.<br><br>Berk<br><br><br>> Date: Thu, 5 Feb 2009 13:07:21 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] heat exchanges<br>> <br>> XAvier Periole wrote:<br>> > <br>> > On Feb 5, 2009, at 11:02 AM, Carlo Camilloni wrote:<br>> > <br>> >> Dear Gromacs users,<br>> >><br>> >> I am doing some tests with thermostats and I would like to know if <br>> >> someone has just done it. In particular:<br>> > I have not done systematic tests but here are my impressions<br>> >><br>> >> 1) How big has to be a protein to be coupled with a separate bath?<br>> > a few residues ...<br>> >><br>> >> 2) Do you know over which time scales a flux of heat is observed <br>> >> between protein and solvent using only one temperature group?<br>> > few 10-100 ps.<br>> This depends a lot on how the rest of the setup is, I would think. I had <br>> some correspondence on the computational chemistry list about this 10 <br>> years ago, and there people boldly stated that with Nose Hoover there is <br>> no need for coupling separate groups at all. At the time I could not <br>> reproduce that with GROMACS, but I did not persevere it. It could also <br>> have to do with flexibility, and/or using united atoms without charges, <br>> i.e. that there is little energetic coupling between e.g. water and a <br>> hydrophobic substance.<br>> <br>> It would be worthwhile to do systematic tests with different thermostats <br>> and coupling schemes. If it turns out that the same problems exist in <br>> Nose Hoover thermostats then it is probably publishable as well.<br>> <br>> <br>> <br>> >><br>> >><br>> >> Thanks,<br>> >><br>> >> Carlo Camilloni<br>> >><br>> >> -- <br>> >> Dr Carlo Camilloni<br>> >> Department of Physics, University of Milano<br>> >> via Celoria, 16 - 20133 Milano, Italy<br>> >> phone: +39-02-50317654<br>> >> carlo.camilloni@mi.infn.it<br>> >> http://merlino.mi.infn.it/~carlo<br>> >><br>> >><br>> >><br>> >><br>> >><br>> >> _______________________________________________<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive at http://www.gromacs.org/search before <br>> >> posting!<br>> >> Please don't post (un)subscribe requests to the list. Use thewww <br>> >> interface or send it to gmx-users-request@gromacs.org.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use thewww <br>> > interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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