fixed bug with Verlet + DD + bonded atom communication

Atoms communicated for bonded interactions can be beyond the cut-off
distance. Such atoms are now put placed in an extra row in the grid.
Fixes #1114

Also improved the performance of the nbnxn grid sorting, especially
for inhomogeneous systems.

Change-Id: Ibe5ba24af95959f5dadd89584e2315da60b55091
Merge "fixed bug with Verlet + DD + bonded atom communication" into release-4-6