Incorporating Hydration Force Determined by Boundary Element Method into Stochastic Dynamics

This paper describes a new method for incorporating the extra mean force terms of solvent including the Coulombic interactions with the induced surface charge and surface pressure of solvent into stochastic dynamics simulation. The boundary element method based on the classical continuum approximation has been used to evaluate those mean force terms. Calculations with our method have been performed on a cyclic undecapeptide cyclosporin A that has been investigated by stochastic dynamics and molecular dynamics in the previous simulations. The detailed analysis has been accomplished in terms of internal hydrogen-bonding forms, conformational fluctuations, and atomic positional correlation function. Compared with the data obtained from previous simulations, our results indicate that the new simulation method presented in this work provides an obvious improvement over the conventional stochastic dynamics simulation technique. This suggests that the average solvent effects should produce a significant influence on the simulated structure and dynamics behavior of biomolecules in aqueous solution.