<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Feb 5, 2009, at 3:33 PM, Berk Hess wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><br><br>> From:<span class="Apple-converted-space"> </span><a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a><br>> To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject: Re: [gmx-users] heat exchanges<br>> Date: Thu, 5 Feb 2009 15:24:28 +0100<br>><span class="Apple-converted-space"> </span><br>><span class="Apple-converted-space"> </span><br>> On Feb 5, 2009, at 3:17 PM, David van der Spoel wrote:<br>><span class="Apple-converted-space"> </span><br>> > Berk Hess wrote:<br>> >> Hi,<br>> >> Strictly speaking you should never have thermostats for separate<span class="Apple-converted-space"> </span><br>> >> 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<span class="Apple-converted-space"> </span><br>> >> different<br>> >> parts of the system in different ways.<br>> >> I think that for most systems only the electrostatics treatment<span class="Apple-converted-space"> </span><br>> >> will have<br>> >> a significant effect. Plain Coulomb cut-off and reaction-field both<span class="Apple-converted-space"> </span><br>> >> produce<br>> >> large integration errors.<br>> the problem is due to errors with berendsen bath which eats up the<br>> water and therefore the protein gets cooled down while it does not need.<br>> The separation avoid this.<br>> I think links/shake have similar effects.<br><br>No, this problem is not due to the Berendsen thermostat.</div></span></blockquote>you are right, I used a mental short cut. </div><div>The Berendsen coupling does not make mistakes :)) but it corrects them. </div><div><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><br>The integrations errors in the electrostatics have much more effect<br>on the water than on the protein, because the water has higher charges<br>and is far more mobile. No thermostat can correct for these errors,<br>unless you use multiple groups.<br>In addition the Berendsen thermostat will move energy from fast to<br>slow motions. This effects becomes much stronger when the thermostat<br>has to do a lot of scaling due to the heat generated by cut-off's.<br><br>Inaccurate constraining will remove heat from the system, but this<br>effect is orders of magnitude smaller than the Coulomb cut-off heating.</div></span></blockquote>ok, good to know.<br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; "><br><br>Berk<br><br>> >> With PME you should never need multiple t-coupl groups.<br>> >> The other issue is slow heat exchange between different parts of<span class="Apple-converted-space"> </span><br>> >> the system.<br>> >> For a protein in solvent I think this is never an issue. But for<span class="Apple-converted-space"> </span><br>> >> other systems<br>> >> it could be. Here it is the question if your simulation is much<span class="Apple-converted-space"> </span><br>> >> 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<span class="Apple-converted-space"> </span><br>> >> Berendsen,<br>> >> since we have v-rescale and Nose-Hoover.<br>> >> I think you can always use PME, v-rescale or nose-hoover and a single<br>> >> t-coupling group.<br>> > I think you are correct, but if someone does the test it can<span class="Apple-converted-space"> </span><br>> > probably be published, if you combine it with recommendations for<span class="Apple-converted-space"> </span><br>> > an equilibration protocol.<br>> ><br>> >> Berk<br>> >> > Date: Thu, 5 Feb 2009 13:07:21 +0100<br>> >> > From:<span class="Apple-converted-space"> </span><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> >> > To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><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<span class="Apple-converted-space"> </span><br>> >> 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<span class="Apple-converted-space"> </span><br>> >> 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<span class="Apple-converted-space"> </span><br>> >> think. I had<br>> >> > some correspondence on the computational chemistry list about<span class="Apple-converted-space"> </span><br>> >> this 10<br>> >> > years ago, and there people boldly stated that with Nose Hoover<span class="Apple-converted-space"> </span><br>> >> there is<br>> >> > no need for coupling separate groups at all. At the time I could<span class="Apple-converted-space"> </span><br>> >> not<br>> >> > reproduce that with GROMACS, but I did not persevere it. It could<span class="Apple-converted-space"> </span><br>> >> also<br>> >> > have to do with flexibility, and/or using united atoms without<span class="Apple-converted-space"> </span><br>> >> charges,<br>> >> > i.e. that there is little energetic coupling between e.g. water<span class="Apple-converted-space"> </span><br>> >> and a<br>> >> > hydrophobic substance.<br>> >> ><br>> >> > It would be worthwhile to do systematic tests with different<span class="Apple-converted-space"> </span><br>> >> thermostats<br>> >> > and coupling schemes. If it turns out that the same problems<span class="Apple-converted-space"> </span><br>> >> 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>> >> > >><span class="Apple-converted-space"> </span><a href="mailto:carlo.camilloni@mi.infn.it">carlo.camilloni@mi.infn.it</a><br>> >> > >><span class="Apple-converted-space"> </span><a href="http://merlino.mi.infn.it/~carlo">http://merlino.mi.infn.it/~carlo</a><br>> >> > >><br>> >> > >><br>> >> > >><br>> >> > >><br>> >> > >><br>> >> > >> _______________________________________________<br>> >> > >> gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> >> > >><span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> >> > >> Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span><br>> >> before<br>> >> > >> posting!<br>> >> > >> Please don't post (un)subscribe requests to the list. Use thewww<br>> >> > >> interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> >> > >> Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> >> > ><br>> >> > > _______________________________________________<br>> >> > > gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> >> > ><span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> >> > > Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span><br>> >> before posting!<br>> >> > > Please don't post (un)subscribe requests to the list. Use thewww<br>> >> > > interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> >> > > Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> >> ><br>> >> ><br>> >> > --<br>> >> > David van der Spoel, Ph.D., Professor of Biology<br>> >> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala<span class="Apple-converted-space"> </span><br>> >> University.<br>> >> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:<span class="Apple-converted-space"> </span><br>> >> +4618511755.<br>> >> > <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a><span class="Apple-converted-space"> </span><a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>> >> > _______________________________________________<br>> >> > gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> >> ><span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> >> > Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before<span class="Apple-converted-space"> </span><br>> >> posting!<br>> >> > Please don't post (un)subscribe requests to the list. 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