Recently, the combination of state-of-the-art molecular mechanical force fields with continuum solvation models enables us to make relatively accurate predictions of both structures and free energies for macromolecules from molecular dynamics trajectories. The first part of this review is focused on the history and basic theory of free energy calculations based on physically effective energy functions. The second part illustrates the applications of free energy calculations on many biological

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... stems, including proteins, DNA, RNA, protein-ligand, protein-protein, protein-nucleic acid complexes, etc. Finally, the prospective and possible strategies to improve the techniques of MM-PBSA and MM-GBSA is discussed. Recently, we have developed a set of radius parameters that are consistent to the HF/6-31G* charges. The 404 training set molecules are from our previous work.107 The PBSA free energies with the newly-developed radius sets are