Actually, the "algorithms" are usually fairly straight-forward and well documented integrators for Newtonian dynamics, usually some form of Verlet Integration.

Actually, the "algorithms" are usually fairly straight-forward and well documented integrators for Newtonian dynamics, usually some form of Verlet Integration. The most popular and efficient Molecular Dynamics packages are open source, some GPL (e.g., NAMD, Gromacs). The technology is nowhere near in silico drug design, but we're converging on useful tools to measure important quantities like free energies of binding. Pharmaceutical companies have some interest in this technology, but at this point, don't direct too much effort into atomistic simulations.