Free Energy Simulations with MacroModel

This chapter provides some of the theory behind the powerful simulation method of free energy perturbation calculations, and describes how to perform a free energy perturbation with MacroModel. If you intend to perform free energy perturbations, we strongly recommend that you become familiar with the current literature on this topic (see Literature for FEP Calculations).

Note: The MM2* and MM3* force fields should not be used for Free Energy Perturbation.