Energy landscapes, global optimization and dynamics of the polyalanine Ac(ala)8NHMe
- 8 April 2001
- journal article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 114 (14) , 6443-6454
- https://doi.org/10.1063/1.1343486
Abstract
A parallel searching algorithm using eigenvector-following is used to generate databases of minima and transition states for an all-atom model of The AMBER force field of Cornell et al. [J. Am. Chem. Soc. 117, 5179 (1995)] is employed both with and without a simple implicit solvent. We use a master equation approach to analyze the dynamics of both systems, and relate the results to the potential energy landscapes using disconnectivity graphs.
Keywords
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