Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics.

Alchemical free energy simulations are commonly used to calculate relative binding or solvation free energies in molecular systems. The convergence of alchemical free energy calculations is often hampered by inefficient sampling of the conformational degrees of freedom, which remain trapped in metastable substates. Here, we show that thermodynamic integration (TI) or free energy perturbation (FEP) can be combined with the recent driven adiabatic free energy dynamics (dAFED) method, in order to enhance conformational sampling along a set of chosen collective variables. The resulting TI-dAFED or FEP-dAFED methods are validated on a two-dimensional analytical problem. The ability of these methods to provide accurate free energy differences for realistic molecular systems is demonstrated by calculating the enantiomerization free energy of the alanine dipeptide in explicit solvent.