Reproduction of the potential of mean force by a modified solvent-accessible surface method

Calculation of the potential of mean force of solute molecules in a solvent is a basic task for understanding many phenomena in solutions. Protein-protein interactions in water are, however, far from fully understood even with the latest supercomputers. In this paper we propose an empirical method to obtain the potential of mean force of solute molecules by means of a modified solvent-accessible-surface (modified SAS) method which is based on the molecular dynamics simulations. We took into account the energy contribution of generating an excluded volume between adjacent solute molecules in the SAS method proposed by Eisenberg et al. The proposed method was examined on the potentials of mean force (pmf's) of methane-methane, octane-octane, carbon-oxygen (methane-water) and oxygen-oxygen (water-water) in water and successfully reproduced the pmf's. This method is basically applicable to general molecular interactions, such as protein-protein interactions in water.