Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side...

Simple analytical functions consisting of electrostatic, polarization, Lennard-Jones or modified Lennard-Jones, and cavity terms are proposed to express the potentials of mean force analytically for spherical particles interacting in water. The cavity term was expressed either through the molecular-surface area of the solute or by using the Gaussian-overlap model of hydrophobic hydration developed in paper 1 of this series. The analytical expressions were fitted to the potentials of mean force of a methane homodimer, heterodimers composed of a methane molecule, and an ammonium cation or a chloride anion, respectively, and dimers consisting of two chloride anions, two ammonium cations, or a chloride ion and an ammonium cation. The potentials of mean force for these dimers were determined by umbrella-sampling molecular dynamics simulations with the AMBER 7.0 force field with TIP3P water either in our earlier work or in this work. For all systems, the analytical formulas fitted the potentials of mean force very well. However, using the molecular-surface area to express the cavity term provided a good fit only when the nonbonded interactions were expressed by an all-repulsive modified Lennard-Jones potential but also resulted in non-physical values of some of the parameters. Conversely, the use of our new Gaussian-overlap-based expression for the cavity term provided a good fit to the potentials of mean force (PMFs) with Lennard-Jones nonbonded potential, and the values of all parameters were physically reasonable.