H5MD - proposal 102: Storage of charges

status: draft

Objective

This proposal aims at defining the storage of the charge associated with each particle.

Motivations

Charge data is missing from H5MD 1.0. It is, at the very least, useful for atomic-level simulations. The interpretation of the value depends however on the situation.

See the original request and the subsequent discussion http://thread.gmane.org/gmane.science.simulation.h5md.user/685

This proposal does not list explicitly all use cases but clarifies the most common interpretations.

Comparison to other file formats

MOSAIC

The Mosaic format relies on so-called conventions to clarify the interpretation of data elements. See the article on MOSAIC http://dx.doi.org/10.1021/ci400599y and the Mosaic PDB convention.

Other file formats

Currently, no other file format clarifies the meaning of the charge data element.

Data in particles group

charge

An element that contains the charge associated to each particle as a scalar, of Integer or Float type.

charge has the optional attribute type of fixed-length string datatype and of scalar dataspace, possible values are effective and formal. In the case effective, the charge is part of an effective description of the interactions with the precise meaning depending on the underlying empirical force fields or coarse-grained models.

In the case formal, the charge is the so-called “formal charge” assigned to an atom (see http://en.wikipedia.org/wiki/Formal_charge) and must be of Integer type. This case corresponds to the entries in PDB files (see definition in the PDBx/mmCIF dictionary http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_atom_site.pdbx_formal_charge.html).

If none of effective or formal describes the data properly, the attribute type may be omitted.