Re: [h5md-user] Additional properties of particles

[Felix Höfling]

Am 01.12.2014, 15:04 Uhr, schrieb Pierre de Buyl
<address@hidden>:

> I didn't think that we would need a full proposal for charges as it  
> would be
> just an additional field. To remove the ambiguity about the kind of  
> charges, I
> have put a proposal :-)
>
> It is not yet generated on the official homepage but github renders the  
> markdown
> at  
> https://github.com/h5md/h5md/blob/master/proposals/0102_particles_charge.mdwn
>
> Cheers,
>
> Pierre

Hi Pierre,

Thanks for putting a proposal on this! I fully support it, but have some
minor questions/comments:

- Why do you use "real" for the formal charge? We could simply use
"formal" (and say that this kind of charge is meant if nothing else is
specified?)

- In the case of force fields, is the charge unique to the particle or to
the bond? Perhaps, it would be best to specify force-field bonds as a
whole (outside of particles/), including all parameters (partial charges,
bond length, bond stiffness, ...). If I understand the concept of force
fields correctly, there is only a finite (albeit large) number of such
parameter sets, and the bonds depends on the atoms involved and their
position within the protein.

- we should have in mind that colloids can have screened charges as well,
e.g., in the DLVO theory:
http://en.wikipedia.org/wiki/DLVO_theory
But as far as I see, the "real" charge enters there. At least, it is a use
case where it makes sense to define the charge as a particle property (and
not as bond/interaction property)

- there is a typo after "formal charge"

BTW, I like the "occupancy" field in the PDB:
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_atom_site.occupancy.html

Cheers,

Felix