If you just have two H atoms, nothing else then the only forces acting are gravity and interatomic forces, in particular, the van-der-waals force (note slide 5 which says the van der waals potential is applicable to monatomic gases) . The van der walls force varies and the inverse sixth power, so it will be zero until the hydrogen atoms are quite close, so weak ol' gravity will be doing most of the work until then.
So, you should set up your potential around the center of mass of the system with U including the gravitational and van-der-waals potentials. For all but the closest distances, be prepared for very slow dynamics.
If you don't know how to use potentials, then take the negative of the derivative of the potential for the van der waals and then add in the force of gravity, both acting in the same direction.