Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy.

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Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, methodology): “Typically, three independent MD simulations for the complex, free protein and free ligand may be performed with a molecular mechanics force field and an explicit solvent model, with the three generated trajectories as the basis for calculating the above free energy contributions [220].”
Combining docking and molecular dynamic simulations in drug design (2006, methodology): “Although only a single MD simulation of the complex is commonly used to determine the conformational free energy, 145 as the structures for both the free ligand and ligand-free protein molecules are extracted from the simulation for the protein–ligand complex, this approach might not be the best.”
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities (2015, methodology): “On the other hand, it ignores the change in structure of the ligand and the receptor upon ligand binding, which may be important factors for the affinity [22].”