erikm at xray.bmc.uu.se
Thu May 3 16:13:52 CEST 2007
3 maj 2007 kl. 15.42 skrev Mark Abraham:
> Jiang ran wrote:
>> Hello everybody,
>> Thank you all for your suggestions ,
>> I red the Gromacs software package manual but found that PVT was
>> 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.
> I don't think you can set up a non-trivial ensemble where both
> and volume are constant, and even if you can, no force fields have
> parameterized for it because there's no physical system in which it is
> true. Consider an ideal gas in such an ensemble. PV = nRT, so with
> P, V
> and n constant, then T is also constant, which means your gas
> can only interact in a way such that kinetic energy is constant.
> Now for constant n and V you could define negative feedback algorithm
> that returned P to a reference pressure, which will force T to vary
> inversely. What's the point in doing that?
Actually, Jiang never mentioned constant n. Particle insertion of
some sort could enable the PVT ensemble. Such operations aren't
exactly trivial, however, and could easily mess up the dynamics of
the protein much more than non-constant P or V.
>> 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
>> way both volume as pressure are conserved. In which file of the
>> software package I can best start implementing it ?
>> I started looking in mdrun.c however this didn't make much sence
>> to me.
> There's no shortcut possible here, as I said some other time in the
> week. Start with the main function and follow through a typical
> calculation - even use a debugger to make life easy on yourself.
> Learn a
> bit about how gromacs works by running a simulation with it first.
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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