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 Poi sson-Boltzmann model supplemented with apolar terms. Our purpose is to study the effects of the model parameters, such as the friction const ant and the size of the electrostatic finite difference grid, on the r ate of conformational sampling and on the accuracy of the resulting fr ee energy map, For dialanine, a converged Ramachandran map is produced in significantly less time than what is required by stochastic dynami cs or Monte Carlo alone. MC/SD is also shown to be faster, per timeste p, than explicit methods. (C) 1997 John Wiley & Sons, Inc.