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<br><br>> Date: Thu, 26 Apr 2007 15:52:10 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] PVT-simulation<br>> <br>> Jiang ran wrote:<br>> > Hello everybody,<br>> > My name is called Jiong and I'm new to the GROMACS simulation software <br>> > package and the field of MD.<br>> > I have some few question:<br>> > <br>> > I would like to simulate a protein in a water box in the PVT-ensemble. <br>> > How to correctly set up such a system in GROMACS ? I already have a itp <br>> > file for my system.<br>> > <br>> <br>> do you mean NPT or NVT?<br>> <br>> read manuals and tutorials please..<br>> <br>> -- <br>> David.<br>> ________________________________________________________________________<br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>> Dept. of Cell and Molecular Biology, Uppsala University.<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br><br>Hello everybody,<br><br>Thank you all for your suggestions ,<br>I red the Gromacs software package manual but found that PVT was not implemented yet in the Gromacs software package. I want to conserve both volume and pressure because my professor says that they are both important for the dynamics of the protein. So I would like to start implementing it for the weekend.<br>I head the idea to introduce langevin dynamics on the atoms close to the boundary so the magnitude of the random force satisfy the fluctuation dissipation theorem, however the net inwarded direction of the total force on each plane will be solved with a set of langrance multipliers such that the net inwarded force on the plane gives the correct reference pressure such that P_ref=-sum(F_plane)/A . In this way both volume as pressure are conserved. In which file of the gromacs software package I can best start implementing it ?<br>I started looking in mdrun.c however this didn't make much sence to me. <br><br>Thank you very much,<br><br>best greetings<br><br>Ran Jiang<br><br><br><br><br><br><br><br><br><br><br><br>> phone: 46 18 471 4205 fax: 46 18 511 755<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<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 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 />Discover the new Windows Vista <a href='http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE' target='_new'>Learn more!</a></body>
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