Computational methods available for the calculation of relative and absolute binding affinities (free energy simulations, continuum electrostatics, linear interaction energy approximations, and empirical solvation models) are reviewed together with recent applications to biological systems. The decomposability of the binding free energy into physically meaningful components is examined and resu...

We measure the solvation free energy, Δμ*, for hard spheres and Lennard-Jones particles in a number of artificial liquids made from modified water models. These liquids have reduced hydrogen bond strengths or altered bond angles. By measuring Δμ* for a number of state points at P = 1 bar and different temperatures, we obtain solvation entropies and enthalpies, which are related to the temperatu...

We describe atomistic simulations of the free energy and entropy of hydration of ions in aqueous solution at 25 °C using a simple point charge model ~SPC/E! for water and charged spherical Lennard-Jones solutes. We use a novel method with an extended Lagrangian or Hamiltonian in which the charge and the size of the ions are considered as dynamical variables. This enables us to determine thermod...

Mean spherical approximation (MSA) for electrolyte solution has been extended to investigate the role of partial solvent polarization densities around an ion in a completely asymmetric binary dipolar mixture. The differences in solvent diameters, dipole moments, and ionic size are incorporated systematically within the MSA framework in the present theory for the first time. In addition to the c...

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 t...

The interface between the vapor and liquid phase of quadrupolar-dipolar fluids is the seat of an electric interfacial potential whose influence on ion solvation and distribution is not yet fully understood. To obtain further microscopic insight into water specificity we first present extensive classical molecular dynamics simulations of a series of model liquids with variable molecular quadrupo...

Using grand-canonical molecular dynamics simulations and free energy calculations of spherical molecular confined films, we investigate the internal energy and entropic origins of density layering and solvation force oscillations. We show that these properties, as well as diffusion and rheological characteristics of such films, depend on interfacial commensurability, with commensurate films exh...

Free-energy calculations in the framework of classical molecular dynamics simulations are nowadays used in a wide range of research areas including solvation thermodynamics, molecular recognition, and protein folding. The basic components of a free-energy calculation, that is, a suitable model Hamiltonian, a sampling protocol, and an estimator for the free energy, are independent of the specifi...