Add support to generate velocities

[splenz]

Currently, the builders initialize velocities to zero. We should add support to the main branch (amber) and martini branch to generate velocities.

We can choose to do this in two ways:

• In the runner, check if all velocities are zero. If they are, call the appropriate method on the simulation object to generate the velocities.
• Just generate the velocities from the Maxwell-Boltzmann distribution