SAMPLING POTENTIAL-ENERGY SURFACE OF GLYCYL GLYCINE PEPTIDE - COMPARISON OF METROPOLIS MONTE-CARLO AND STOCHASTIC DYNAMICS

A comparative study was carried out to test the efficiency with which Metropolis Monte Carlo (MC) and stochastic dynamics (SD) sample the po tential energy surface of the N-acetyl glycyl glycine methylamide pept ide as defined by the united atom AMBER force field. Boltzmann-weight ed ensembles were generated with variations of all internal degrees of freedom (i.e., stretch, bend, and torsion) for a single N-acetyl glyc yl glycine methylamide molecule at 300 K by 10(8)-step MC and 100-ns S D simulations. As expected, both methods gave the same final energetic results. However, convergence was found to be similar to 10 times fas ter with MC than with SD as measured by comparisons of the populations of all symmetrically equivalent conformers. (C) 1998 John Wiley & Son s, Inc.