[gmx-users] Output per-group kinetic energy

[Anthony Costa]

On Wed, Sep 15, 2010 at 09:15, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> g_traj constraints
>
> turns up tons of results, among which are a few useful ones:
>
> http://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html
> http://lists.gromacs.org/pipermail/gmx-users/2002-August/002244.html
>
> Surely, with a bit more digging, you can find some directly related to
> kinetic energy.  I'm quite sure I've seen them, but a good deal of time has
> passed.
>
> -Justin

Thanks again, but I think I wasn't clear in my question. Certainly
g_traj doesn't know about constraints. My interest in kinetic energy
was only an example, I'm hoping for a general solution for other
quantities. I'd also like to output, say, the potential or total
energies per molecule. Obviously the potential is a bit more complex
than the kinetic for each molecule, but there's no reason why it
shouldn't be able to be calculated given that all the pairwise
energygroup interactions are known and the instantaneous
configurations are known.

On another completely separate note, my understanding is that
calculation of the Hessian can only be done for normal mode analysis
around a minimum, and it can not be calculated on the fly during a
trajectory. Is this correct, and has anyone out there found a method?
Perhaps these things are simply too specialized and I'll have to write
them myself, but since the curvature of phase space would be
calculatable within the force loops for a given potential, and Hessian
calculations are already implemented for normal mode analysis, I don't
see any reason why this would be too difficult to implement. Any
thoughts would be most welcome.

Thanks again,
Anthony