A one-way shooting algorithm for transition path sampling of asymmetric barriers.
We present a novel transition path sampling shooting algorithm for the efficient sampling of complex (biomolecular) activated processes with asymmetric free energy barriers. The method employs a fictitious potential that biases the shooting point toward the transition state. The method is similar in spirit to the aimless shooting technique by Peters and Trout [J. Chem. Phys. 125, 054108 (2006)], but is targeted for use with the one-way shooting approach, which has been shown to be more effective than two-way shooting algorithms in systems dominated by diffusive dynamics. We illustrate the method on a 2D Langevin toy model, the association of two peptides and the initial step in dissociation of a β-lactoglobulin dimer. In all cases we show a significant increase in efficiency.
Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
Z Faidon
ZF
Brotzakis
Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
Peter G
PG
Bolhuis
D000465:Algorithms; D004058:Diffusion; D019281:Dimerization; D007782:Lactoglobulins / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*
D007782:Lactoglobulins; D010455:Peptides