Save excluded non-bonded interactions in .tpr file

Save excluded non-bonded interactions in .tpr file

The intermolecularExclusionGroup of the molecular topology (mtop) has
not been saved in the tpr file before, which lead to the unexpected
behviour that an mtop as set up in grompp was not available in the same
state when the simulation was started.

Excluding non-bonded interactions of a group with the rest of the system
is currently needed for the QM/MM implementation. This change will allow
to complete system setup for simulations that need to exclude non-bonded
interactions at grompp time instead when starting the simulation.

refs #3172

Change-Id: Ia0e3f0571fa467337664bedec2e91a5a008507ca