Re: [h5md-user] Additional properties of particles

[Pierre de Buyl]

(...)

On Fri, Nov 07, 2014 at 10:53:29AM +0100, Konrad Hinsen wrote:
> Charge may superficially seem to be a per-particle physical property.
> This is in fact true for protons and electrons, and even ions, but not
> for atoms that are parts of molecules, with covalent bonds. The
> so-called "partial charges" in Molecular Mechanics force fields are
> fit parameters in a rather crude approximation used to describe
> electrostatic interactions in molecular systems. They make sense only
> as part of a complete force field definition that describes *all*
> interactions, because often compromises are made by modifying one type
> of interaction to get a better fit for another one.

As far as molecular data is concerned, this superficial approach to storing the
charges is just fine, no? At the molecular level, this is all that I would
expect. While it is true that it is less unambiguous (note the double negative)
than the position, for instance, it remains a common quantity that one wants to
store. It can be fixed in time (most FF) or even change (ReaxFF, for instance).

The interpretation remains to the final user exactly as for "species" and
"charge" sould be included in my opinion.

(...)

> MOSAIC is, in fact, one such bookkeeping convention, and the
> H5MD+MOSAIC convention provides a complete solution for handling
> molecular structure and connectivity. It also permits storing force
> field parameters, including partial charges. In the current version it
> does not provide time-dependent charges though.

Is the definition of force fields part of MOSAIC yet?

Pierre