Simulated annealing is included to aid in locating global, rather than subsidiary, energy minima. In this process the random dense gas starting model is not initially fully optimized. This agitation kicks the energy to a higher value, where optimization is resumed. This process may be repeated many times. Finally the temperature is decreased to zero to give the predicted structure.
Molecular docking is simply a case of a small hetero cluster.
For instance, a sample calculation is available which predicts the docking of two deoxyguanosine molecules with actinomycin to form a hetero 3-cluster. The program will also handle molecular docking in the crystalline context by simply specifying two different molecules in the asymmetric unit. Program mpa does allow the possibility of intramolecular flexibility by allowing rotation about selected bonds.