Change get_atom_index to allow multiple molecules.

Change get_atom_index to allow multiple molecules.

Make gromacs take into account atoms in all molecules.
This allows Hessian matrix creation to work over all
molecules in a simulation. An update to the regression
tests has been submitted as well.

During fixing of the problem, another problem surfaced in
the normal mode calculations to do with ordering of atoms
which is fixed here as well.

Fixes #2720

Change-Id: I9fc2dd05cb1c67d46b6d4c3d9139e6b3bed72f17