Molecular dynamics simulations of ionic systems require the inclusion of long-range electrostatic forces. We propose an expression for the long-range electrostatic forces based on an analytical solution of the Poisson–Boltzmann equation outside a spherical cutoff, which can easily be implemented in molecular simulation programs. An analytical solution of the linearized Poisson–Boltzmann (PB) equation valid in a spherical region is obtained. From this general solution special expressions are derived for evaluating the electrostatic potential and its derivative at the origin of the sphere. These expressions have been implemented for molecular dynamics (MD) simulations, such that the surface of the cutoff sphere around a charged particle is identified with the spherical boundary of the Poisson–Boltzmann problem. The analytical solution of the Poisson–Boltzmann equation is valid for the cutoff sphere and can be used for calculating the reaction field forces on the central charge, assuming a uniform continuum of given ionic strength beyond the cutoff. MD simulations are performed for a periodic system consisting of 2127 SPC water molecules with 40 NaCl ions (1 molar). We compare the structural and dynamical results obtained from MD simulations in which the long range electrostatic interactions are treated differently; using a cutoff radius, using a cutoff radius and a Poisson–Boltzmann generalized reaction field force, and using the Ewald summation. Application of the Poisson–Boltzmann generalized reaction field gives a dramatic improvement of the structure of the solution compared to a simple cutoff treatment, at no extra computational cost.

A new nonpolarizable force field for mixtures of urea and water is described. The model was parametrized to reproduce the experimental Kirkwood-Buff integrals between urea-urea, urea-water, and water-water pairs, as defined by the Kirkwood-Buff theory of solution mixtures. It was observed that the integrals were sensitive to the charge distribution used, and that none of the literature charge distributions investigated produced the correct degree of urea association. However, a hybrid charge distribution was found which accurately reproduced the integrals over a range of concentrations. Correspondingly, the solution thermodynamics, including the activity of urea, were well described. In addition, other physical properties (density, diffusion constants, compressibility) were also well reproduced. The model displayed little or no urea self-aggregation, in agreement with the experimental data. The ideal nature of urea mixtures (molar activity scale) appeared to result from a balance between water-water and urea-water interactions, with a smaller urea-urea interaction. Although developed for use with SPC/E water, the new model performed equally well with the SPC and TIP3P water models.

A force field for the simulation of mixtures of sodium chloride and water is described. The model is specifically designed to reproduce the experimentally determined Kirkwood–Buff integrals as a function of salt concentration, ensuring that a good representation of the solution activity is obtained. In addition, the model reproduces many of the known properties of sodium chloride solutions including the density, isothermal compressibility, ion diffusion constants, relative permittivity, and the heat of mixing. The results are also compared to other common sodium chloride force fields.

Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using simple binding models. More recently, a renewed interest in the use of Kirkwood-Buff (KB) theory to analyze solution mixtures has provided new information on the effects of osmolytes and denaturants and their interactions with biomolecules. Here we review the status of KB theory as applied to biological systems. In particular, the existing models of denaturation are analyzed in terms of KB theory, and the use of KB theory to interpret computer simulation data for these systems is discussed.