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Inspired by the recent development on calculating the free energy change via a relaxation process [Nat. Phys. 14, 842 (2018)], we investigate the role of heat released in an irreversible relaxation following a large perturbation. Utilizing a derivation without microscopic reversibility, we arrive at a new free energy estimator that employs a volume term to account for missing important rare events. Applications to harmonic oscillators and particle insertion in Lennard-Jones fluid agree well with the (numerical) exact solutions. Our study hence suggests an alternative interpretation to the insufficient sampling problem in free energy calculations.
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential. The converg
The free energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path followed
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation correctio
It has recently been observed [Phys. Rev. Lett. 113, 113002 (2014)] that the ground-state energy may be obtained directly as a simple sum of augmented Kohn-Sham orbital energies, where it was ascertained that the corresponding one-body shifted Kohn-S
The Alchemical Transfer Method (ATM) for the calculation of standard binding free energies of non-covalent molecular complexes is presented. The method is based on a coordinate displacement perturbation of the ligand between the receptor binding site