A simulation method of combinding boundary element method with generalizedLangevin dynamics

A new simulation approach to incorporate hydration force into generalized L angevin dynamics (GLD) is developed in this note. The hydration force deter mined by the boundary element method (BEM) is taken into account as the mea n force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model i s taken for the friction kernel. A simulation study has been performed on t he cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dyn amics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.