Hybrid Hamiltonian replica exchange molecular dynamics simulation method employing the Poisson–Boltzmann model

Abstract

A hybrid Hamiltonian replica exchange molecular dynamics simulation scheme based on explicit water model hybrided with Poisson-Boltzmann model is brought out. In this method the motions of atoms are governed by potential energy obtained from explicit water model. However, the exchanges between different replicas under different temperatures are controlled by the solvation energies of the solute calculated using the Poisson-Boltzmann model. In order to get the correct canonical ensembles, the van der Waals radii, which are used to define the dielectric boundary, have to be optimized. The conformational spaces of three distinct pentapeptides, Met-enkephalin, alanine 5, and glycine 5, are explored. We find that with the optimized radii the structural ensembles are nearly identical to those obtained by standard replica exchange simulations while the number of replica needed is reduced greatly.