> Date: Thu, 26 Apr 2007 15:52:10 +0200> From: [EMAIL PROTECTED]> To:
> [email protected]> Subject: Re: [gmx-users] PVT-simulation> > Jiang ran
> wrote:> > Hello everybody,> > My name is called Jiong and I'm new to the
> GROMACS simulation software > > package and the field of MD.> > I have some
> few question:> > > > I would like to simulate a protein in a water box in the
> PVT-ensemble. > > How to correctly set up such a system in GROMACS ? I
> already have a itp > > file for my system.> > > > do you mean NPT or NVT?> >
> read manuals and tutorials please..> > -- > David.>
> ________________________________________________________________________>
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,> Dept. of
> Cell and Molecular Biology, Uppsala University.> Husargatan 3, Box 596,
> 75124 Uppsala, SwedenHello everybody,Thank you all for your suggestions ,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.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 ?I started looking in mdrun.c however this didn't
> make much sence to me. Thank you very much,best greetingsRan Jiang> phone:
> 46 18 471 4205 fax: 46 18 511 755> [EMAIL PROTECTED] [EMAIL
> PROTECTED] http://folding.bmc.uu.se>
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