Re: [h5md-user] Additional properties of particles

[Pierre de Buyl]

On Fri, Nov 28, 2014 at 01:36:16PM +0100, Pierre de Buyl wrote:
> (...)
> 
> 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.

A "module" or an attribute could be used to make the distinction between charges
and partial charges. Are there more subtleties related to charges?

> (...)
> 
> > 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
> 
> 

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Pierre de Buyl
KU Leuven - Institute for Theoretical Physics
W http://pdebuyl.be/
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