An efficient molecular dynamics simulation method for calculating the diffusion-influenced reaction rates

An efficient molecular dynamic (MD) method was proposed to calculate the time-dependent rate coefficient for diffusion-influenced bimolecular reactions. The applicability of the proposed method is limited to the case with low reactant concentration, but the rate of reactions involving large molecules of complicated geometry can also be calculated within a unified framework. The subtle dynamic solvent effects that cannot be explained within the simple diffusion equation description were investigated using the MD method. Comparison of diffusive and inertial BD simulation results shows that the effect of finite velocity relaxation time of reactant molecules persists up to the steady state.