reorganization, added a water unit test, and velocity handling

Some gromacs reorganization for nonbondeds, and moving even some
short sections into their own functions.

Better handling of no velocities.  In gromacs, there is a difference between
zero velocities and no velocities, so now zero velocities are stored as None,
and for now, if those are none in LAMMPS and DESMOND, they are interpreted as zero.

Added a water unit test and did some bugfixing resulting from errors there.