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Yes, but that is done before starting the simulation, so your total energy<br>will still be nicely constant.<br><br>Berk<br><br>> Date: Mon, 14 Jun 2010 11:55:18 +0200<br>> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of liquid         mixtures<br>> From: tsjerkw@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Hey :)<br>> <br>> Errm, you subtract the overall linear momentum. That affects the<br>> kinetic energy, decreasing it, doesn't it?<br>> <br>> Tsjerk<br>> <br>> On Mon, Jun 14, 2010 at 10:59 AM, Berk Hess <gmx3@hotmail.com> wrote:<br>> > Hi,<br>> ><br>> > Why not?<br>> ><br>> > Berk<br>> ><br>> >> Date: Mon, 14 Jun 2010 08:19:30 +0200<br>> >> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of<br>> >> liquid mixtures<br>> >> From: tsjerkw@gmail.com<br>> >> To: gmx-users@gromacs.org<br>> >><br>> >> Hi Godwin,<br>> >><br>> >> I noticed you're removing center of mass motion, which you shouldn't for<br>> >> NVE.<br>> >><br>> >> Cheers,<br>> >><br>> >> Tsjerk<br>> >><br>> >> On Mon, Jun 14, 2010 at 4:09 AM, Godwin Kanu <biggugo@live.com> wrote:<br>> >> ><br>> >> > Hi GMX Users,<br>> >> ><br>> >> > I am having difficulties getting gromacs to conserve energy (I<br>> >> > experience a<br>> >> > directional drift) when I do an NVE simulation of mixtures (i tried both<br>> >> > THF/water and water/methanol). But when I do simulation of a pure liquid<br>> >> > it<br>> >> > works great. I have tried tinkering with a lot of stuff including the<br>> >> > electrostatic interaction and making sure the combination rules for<br>> >> > non-bonded interactions work as it is supposed to. I usually start with<br>> >> > an<br>> >> > NVT simulation to equilibriate it at the temperature I'm interested in<br>> >> > before removing the temperature bath to do an equilibration run in<br>> >> > the microcanonical ensemble. I have attached some of my input files for<br>> >> > you<br>> >> > to examine. I'm using GROMACS version 4.0.5 parallel.<br>> >> > Thanks<br>> >> ><br>> >> > Godwin.<br>> >> ><br>> >> ><br>> >> ><br>> >> > ________________________________<br>> >> > Hotmail has tools for the New Busy. Search, chat and e-mail from your<br>> >> > inbox.<br>> >> > Learn more.<br>> >> > --<br>> >> > gmx-users mailing list gmx-users@gromacs.org<br>> >> > http://lists.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 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>> >><br>> >><br>> >><br>> >> --<br>> >> Tsjerk A. Wassenaar, Ph.D.<br>> >><br>> >> post-doctoral researcher<br>> >> Molecular Dynamics Group<br>> >> Groningen Institute for Biomolecular Research and Biotechnology<br>> >> University of Groningen<br>> >> The Netherlands<br>> >> --<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://lists.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>> > ________________________________<br>> > New Windows 7: Find the right PC for you. Learn more.<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.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>> <br>> <br>> <br>> -- <br>> Tsjerk A. Wassenaar, Ph.D.<br>> <br>> post-doctoral researcher<br>> Molecular Dynamics Group<br>> Groningen Institute for Biomolecular Research and Biotechnology<br>> University of Groningen<br>> The Netherlands<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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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