Energy Landscapes, Global Optimization and Dynamics of the Polyalanine Ac(ala)8NHMe

Paul N. Mortenson and David J. Wales

A parallel searching algorithm using eigenvector-following is used to generate databases of minima and transition states for an all-atom model of Ac(ala)8NHMe. The AMBER force field of Cornell et al. (J. Am. Chem. Soc. 117, 5179) is employed both with and without a simple implicit solvent. We use a master equation approach to analyse the dynamics of both systems, and relate the results to the potential energy landscapes using disconnectivity graphs.