> Date: Thu, 3 May 2007 23:42:28 +1000> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: Re: [gmx-users] PVT-simulation> > Jiang ran
> wrote:> > Hello 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. > > I don't think you can set up a
> non-trivial ensemble where both pressure> and volume are constant, and even
> if you can, no force fields have been> 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 molecules> 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?> > > 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.> > There's no shortcut possible here, as I said some other
> time in the last> 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.>
> > Mark> _______________________________________________> gmx-users mailing
> list gmx-users@gromacs.org>
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> http://www.gromacs.org/mailing_lists/users.phpThank you for your
> suggestion,>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 molecules>can
> only interact in a way such that kinetic energy is constant.Dear mister
> Abraham,Thank you for suggestion and very good theory, However I don't
> understand your theory. An ideal gas is a hypothetical gas consisting of
> identical particles of zero volume, with no intermolecular forces So which
> interactions do you mean ? They do make perfect collisons with wall (which
> don't exist in pbc...right ??).Therefor in my case the only "interactions"
> are with the infinite external temperature, pressure bath (random forces),
> which make sure of the fact that the kinetic energy and pressure are
> constant as the friction term is balancing the random force (fluctuation
> dissipation theorem), so I really don't see the need of a negative feedback
> algorithm here.I was thinking as the langevin forces are external they don't
> play a role in virial. The forces between ideal gas atoms can either be zero
> or infinite. Therefor the internal viral can not be defined for an ideal gas
> in the first place. According to clausius the total viral has now to be equal
> to the kinetic energy tensor. As kinetic energy is known the total virial is
> kown too. The external viral is known (random forces), however the internal
> viral could not be defined in first place. Is this a paradox ? Thank you
> for nice helpfull discussion,greetingsRan Jiang
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