ran_jiong_lang2 at hotmail.com
Thu May 3 17:08:17 CEST 2007
> Date: Thu, 3 May 2007 23:42:28 +1000> From: Mark.Abraham at anu.edu.au> To: gmx-users at 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 at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read 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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