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Re: [h5md-user] Additional properties of particles
From: |
Felix Höfling |
Subject: |
Re: [h5md-user] Additional properties of particles |
Date: |
Fri, 07 Nov 2014 10:34:34 +0100 |
User-agent: |
Opera Mail/12.16 (Linux) |
Hi Jakub,
Am 06.11.2014, 16:11 Uhr, schrieb Jakub Krajniak
<address@hidden>:
Hi,
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/
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
"particle_subgroupX" are H5MD elements, their names match the
corresponding subgroups in particle/ and the contents is a list of IDs (or
just the array index if "id" is not present).
To proceed more efficiently with the discussion, please open an H5MD
proposal as well.
Thanks for contributing!
Best regards,
Felix