Re: [h5md-user] Additional properties of particles

[Konrad Hinsen]

Pierre de Buyl writes:

 > 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.

My point is that the interpretation depends on where these charges
come from, so that information must be storable. That's why I don't like
the idea of just having a property called "charge", without any provenance
information. I am not saying that such provenance information should be
compulsory, but if it exists there should be a clear way to store it.

 > Is the definition of force fields part of MOSAIC yet?

Not yet, this is quite hard to do in a way that is both flexible and
useful with today's scientific software technology. I have a pretty
clear idea of how I will do it, but I don't believe it works until
I have a working implementation.

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

Nothing I can think of immediately. I'd say that all subtleties
can be handled with additional annotation.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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