gmx msd -mol broken
In a simplification of gmx msd a bug was introduced such that the -mol flag does not work anymore. See https://gerrit.gromacs.org/#/c/8789/
Revert "Removed t_topology from gmx msd"
This reverts commit b9e0922af7eccbb4b9110dd0ea99cdac0244a27a.
MSD tests for the -mol option.
Had to free some memory as well to make tests pass.
Added basic code for running grompp.
Renamed spc5 files in simulationdatabase that are used
in src/programs/mdrun/tests to tip3p5 since they were
in fact using tip3p and in this manner a conflict with
the gmx_msd tests is avoided.
TODO: re-use the grompp code in moduletest.cpp
Part of #2815