Documentation VMD parameters

VMD parameters are saved under /parameters/vmd_structure.
Parameters are stored either per atom, per species or per residue.
*If a parameter is stored per atom, then the corresponding dataset has to have a row for each atom. Therefore each atom has a number which can be thought of as atomid. This atomid is equivalent to the row in which the data stands.
*If a parameter is stored per species, then there has to be a dataset /parameters/vmd_structure/indexOfSpecies.
The dataset indexOfSpecies must contain as much rows as there are different species present in /particles/{all groups}/species (where the membership of each atom in the group to a species is saved). (At the moment only time-independent species datasets are supported, since VMD does not really allow to change particle properties per timestep). This indexOfSpecies is equivalent to the row in which the data stands. Then a new property can be stored for each listed species, by creating a dataset for the property with as many rows as there are different species. The row there is again equal to the indexOfSpecies. 
*If a parameter is stored per residue, then there has to be a dataset /parameters/vmd_structure/resid. The dataset resid must contain as much rows as there are atoms. For each atom the membership to a residue is then stored there by assigning a resid. resid is equivalent to the row in which the data stands.
In VMD each atom is explicitly assigned to its properties. This is done by reading out the corresponding properties (through tracing the atomid, indexOfSpecies, resid).

Which properties can be read out by the VMD-H5MD plugin (additional to the ones from the h5md specification) and how they need to be stored can be seen in the section overview. If present these parameters are used for coloring,... if not present, the plugin sets default values.
Coloring is either default (red) or according to data_species[atomid]%112. That means each species gets its own color (modulo 112)


##################Bonds#################
Bonds can be drawn in VMD by defining which two atoms share a bond. 
For each bond the "start atom" and the "end atom" of the bond are defined.
The start atom index of bond number i is saved in the i-th row of /parameters/vmd_structure/bond_from.
The end atom index of bond number i is saved in the i-th row of /parameters/vmd_structure/bond_to.

###################Overview###################
Additional parameters which are not specified in the H5MD specification but which can be read by this plugin.

	   bonds 				/parameters/vmd_structure/bond_from, /parameters/vmd_structure/bond_to
	   char name[16]; -> per species	/parameters/vmd_structure/name
	   char type[16]; -> per species	/parameters/vmd_structure/type     
	   char resname[8]; -> per residue	/parameters/vmd_structure/resname
	   int resid;	-> per atom		/parameters/vmd_structure/resid
	   char segid[8]; -> per atom     	/parameters/vmd_structure/segid
	   char chain[2]; -> per residue     	/parameters/vmd_structure/chain
	   float radius; -> per species		/parameters/vmd_structure/radius       
	   int atomicnumber; (allowed in range 0 to 112) -> per species	/parameters/vmd_structure/atomicnumber