grompp now retains the order of bonds converted to constraints

grompp now retains the order of bonds converted to constraints

With the constraint mdp option grompp used to write tpr files where
the order of the constraints was reversed with respect to the order
of the bonds. This reordering has been removed.

Change-Id: I094c5001ccad1e80f46b61c4fbcfa400fd5c1e74