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.