INCORPORATING HYDRATION FORCE DETERMINED BY BOUNDARY-ELEMENT METHOD INTO STOCHASTIC DYNAMICS

This paper describes a new method for incorporating the extra mean for ce terms of solvent including the Coulombic interactions with the indu ced surface charge and surface pressure of solvent into stochastic dyn amics simulation. The boundary element method based on the classical c ontinuum approximation has been used to evaluate those mean force term s. Calculations with our method have been performed on a cyclic undeca peptide cyclosporin A that has been investigated by stochastic dynamic s and molecular dynamics in the previous simulations. The detailed ana lysis has been accomplished in terms of internal hydrogen-bonding form s, conformational fluctuations, and atomic positional correlation func tion, Compared with the data obtained from previous simulations, our r esults indicate that the new simulation method presented in this work provides an obvious improvement over the conventional stochastic dynam ics simulation technique. This suggests that the average solvent effec ts should produce a significant influence on the simulated structure a nd dynamics behavior of biomolecules in aqueous solution.