J Chem Phys. 2006 Sep 21;125(11):114101. doi: 10.1063/1.2335640.

Bias annealing: a method for obtaining transition paths de novo.

The Journal of chemical physics

Jie Hu, Ao Ma, Aaron R Dinner

PMID: 16999460 DOI: 10.1063/1.2335640

Abstract

Computational studies of dynamics in complex systems require means for generating reactive trajectories with minimum knowledge about the processes of interest. Here, we introduce a method for generating transition paths when an existing one is not already available. Starting from biased paths obtained from steered molecular dynamics, we use a Monte Carlo procedure in the space of whole trajectories to shift gradually to sampling an ensemble of unbiased paths. Application to basin-to-basin hopping in a two-dimensional model system and nucleotide-flipping by a DNA repair protein demonstrates that the method can efficiently yield unbiased reactive trajectories even when the initial steered dynamics differ significantly. The relation of the method to others and the physical basis for its success are discussed.

Publication Types

• Journal Article
• Research Support, Non-U.S. Gov't
• Research Support, U.S. Gov't, Non-P.H.S.