[h5md-user] Additional properties of particles

[Konrad Hinsen]

Jakub Krajniak writes:

 > Recently I started to use H5MD (thanks to Pierre de Buyl) but I would like 
 > to 
 > propose additional properties that seems to be missing.
 > 1. The particle charge 'q'. It should behave like the 'mass' property and 
 > could 
 > be both time-dependent and time-independent.
 > 
 > 2. The 'resnr' that will behave like current 'species'. That property should 
 > group the particles in molecules. The .gro and .pdb file format have 
 > something 
 > similar. The residue name is not so important as it could be solved outside 
 > the 
 > h5md.

Please have a look at the H5MD + Mosaic definition, which might well solve
both of your problems:

  
https://mosaic-data-model.github.io/mosaic-specification/h5md_mosaic_module.html

Integrating these two properties as isolated extensions to H5MD is not
trivial and risks making the format difficult to use for more complex
systems.

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.

The "residue number" concept is not physical at all, as Felix pointed
out. It is part of a bookkeeping convention for molecular systems.
Again, there is little point in storing one parameter of one
particular bookkeeping convention. What you want is all the parameters
of a convention, and a general file format shouldn't impose one such
convention at all, given that there are several ones in use.

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.

Konrad.
-- 
---------------------------------------------------------------------
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
---------------------------------------------------------------------