Add a "prototype" of two DPD atoms with velocity-Verlet algorithm.

* step-by-step/in.twoatoms_velocity_verlet:
* step-by-step/twoatoms_velocity_verlet.mac:
Fix a bug in twoatoms.mac, switch communicate->comm_modify
Get rid of `m'
Move in.equal in README
twoatoms_velocity_verlet.mac now agrees with LAMMPS