Internal parameter storage for IMDModules

Internal parameter storage for IMDModules

It is currently not possible for MdModules to store data in a tpr
file that is non-mdp input, e.g., the result of some computation
during setup level.

Atom indices of index groups are one example: evaluated from strings
during grompp time, they are stored as list of integers in the run
input file. During the mdrun setup the information to evaluate the
index groups is no longer available.

This patch introduces a storage for internal MdModule parameters.

The parameters are stored in a seperate key-value-tree in the input
record that is then serialized into the tpr file. In contrast to the
ir->params, this key-value-tree does not match the options given in
an input file.

Change-Id: I207d8c837c39f1afb196507fe228306700e46a49