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Front Mol Biosci. 2018 Feb 8;5:11. doi: 10.3389/fmolb.2018.00011. eCollection 2018.

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.

Author information

1
Dipartimento di Scienze Matematiche, Informatiche e Fisiche, Universita' di Udine, Udine, Italy.
2
Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy.
3
Dipartimento di Area Medica, Universita' di Udine, Udine, Italy.
4
Science and Math Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.

Abstract

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. 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 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. 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. We review briefly the basic theory and discuss the advancements in light of practical applications.

KEYWORDS:

MM/GBSA; continuum solvent; enthalpy; entropy; free energy; implicit solvent; molecular dynamics simulations

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