Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations

Accurate modeling of potential functions is critical for realistic molecular dynamics (MD) simulations. In this study, improvement in potential functions is discussed by revisiting the multistate empirical valence bond (MS-EVB) method and the FUJI force field. The MS-EVB method enables simulation of dynamic chemical reactions in various situations. In this study, excess protons in water under shear were investigated by combining the MS-EVB method with the non-equilibrium MD technique. It was found that the orientation of the hydronium-like moiety is considerably more anisotropic under shear than that of the water molecule. Separately, the FUJI force field includes main-chain torsional parameters carefully derived on the basis of high-level ab initio calculations. To further demonstrate that the use of the FUJI force field improves the accuracy of MD results beyond previously reported examples, the conformational distribution of the Ala dipeptide was investigated. The results obtained using the FUJI force field agreed more closely with the experimental results than those obtained using other standard force fields. Interestingly, the MD trajectories with the FUJI force field undergo the Y conformation more frequently than those with other popular force fields. Furthermore, it was found that the choice of force field affects the structures of an antigen–antibody complex obtained using MD simulations. These improvements in the force fields essentially extend the range of applications for the MD simulation method.