(373d) Easy Transition Path Sampling in the Microcanonical Ensemble

Peters, B., University of California Santa Barbara
Shea, J. E., University of California
Mullen, R. G., University of California

Molecular simulations of chemical reactions, diffusion in solids, protein folding, and nucleation processes require rare events methods. Transition path sampling methods can simulate these processes without disturbing the natural system dynamics.We present a new algorithm for sampling transition paths: permutation shooting. Permutation shooting rigorously preserves the total energy and momentum of the initial trajectory and is simple to implement even for rigid water molecules. Permutation shooting is demonstrated for two systems: (1) vacancy migration in a two-dimensional crystal, and (2) the association of biomolecules in water.