Where R is the gas constant, T the temperature, β is equal to 1 R T, U is the potential energy and ⟨⟩ indicates thermodynamic ensemble average. We review briefly the basic theory and discuss the advancements in light of practical applications. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. 4Science and Math Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emiratesįree energy is the key quantity to describe the thermodynamics of biological systems.3Dipartimento di Area Medica, Universita' di Udine, Udine, Italy.2Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy.
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