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<BR>Hi,<BR>
<BR>
I stopped removing center of mass motion as advised by Tsjerk, but I experience the same problem still. I understand the arguement of subtracting out the momentum, but if this was the sole issue, I should experience the same problem when simulating pure liquids, but I don't. Any more suggestions will be appreciated. <BR>
<BR>
Godwin<BR>
<BR>
<BR><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 />Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. <a href='http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2' target='_new'>See how.</a></body>
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