Re: [h5md-user] Additional properties of particles

[Pierre de Buyl]

Hi,

On Fri, Nov 07, 2014 at 10:34:34AM +0100, Felix Höfling wrote:
> Am 06.11.2014, 16:11 Uhr, schrieb Jakub Krajniak <address@hidden>:
> 
> >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.
> >
> Good suggestion, we should have included the charge already in 1.0,
> but overlooked them as nobody of us was using electrostatic
> interactions. The charge is clearly a per-particle property just as
> mass is. The physical unit of charge is already covered by the
> "units" module.
> 
> To make things concrete, please open an H5MD proposal for including
> the charge:
> http://nongnu.org/h5md/proposals/

It may be a little overwork to include that in a proposal. We could, however,
make a proposal for minor updates like this one.

> >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.
> >
> This point is less clear. The residual number does not affect the
> physical properties/interactions of the particles (unlike "species"
> does), its primary purpose is for analysis. (Please correct me if
> I'm mistaken.)
> 
> I'm not an expert in proteins, but the residuals seem to describe
> the protein structure on a more coarse-grained level. So it has more
> similarities with topology/connectivity (although it is less
> stringent). What comes to mind is to store information about the
> residual groups outside of the particles tree.
> 
> Suggestions: store a list of particle indices (better: IDs) for each
> residual. This makes it easy to look up all particles of given
> residual, however the inverse would be inefficient.
> 
> H5MD root
>  \-- residuals
>       \-- (name)
>           \-- particle_subgroup1
>           \-- particle_subgroup2
> 

As Konrad points out (other subthread), residue definition should be thought
differently than what we have done so far. I don't know yet how it can be
incorporated in H5MD as I don't really work with that kind of systems.

But it maybe that Jakub (?) is interested in reproducing the feature that some
MD packages have that each particle belongs (uniquely, then) to a molecule. This
is not the straightforward translation of a physical property then.

P