Conformational sampling with Poisson-Boltzmann forces and a stochastic dynamics Monte Carlo method: Application to alanine dipeptide

We apply a combination of stochastic dynamics and Monte Carlo methods (MC/SD) to alanine dipeptide, with solvation forces derived from a Poisson-Boltzmann model supplemented with apolar terms. Our purpose is to study the effects of the model parameters, such as the friction constant and the size of the electrostatic finite difference grid, on the rate of conformational sampling and on the accuracy of the resulting free energy map, For dialanine, a converged Ramachandran map is produced in significantly less time than what is required by stochastic dynamics or Monte Carlo alone. MC/SD is also shown to be faster, per timestep, than explicit methods. (C) 1997 John Wiley & Sons, Inc.