title: Reducing the cost of evaluating the committor by a fitting procedure.
abstract: Correct identification of reaction coordinates in complex systems is essential for understanding the mechanisms of their reaction dynamics. Existing methods for identifying reaction coordinates typically require knowledge of the committor--the probability of a given configuration to reach the product basin. The high computational cost of evaluating committors has limited applications of methods for identifying reaction coordinates. We proposed a fitting procedure that can reduce the cost of evaluating committors by an order of magnitude or more. The method only requires evaluating the committors of a few configurations in a transition path by the standard and costly shooting procedure. The committors of the other configurations are then estimated with great accuracy by a sigmoid function derived from fitting the few numerically evaluated committors. The method has been systematically tested on a model system of a Brownian particle moving in a one-dimensional double-well potential, and a small biomolecular system--the isomerization of alanine dipeptide in vacuum and in explicit water.
authors.affiliation: Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan St., Chicago, Illinois 60607, USA.
authors.forename: Wenjin
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan St., Chicago, Illinois 60607, USA.
authors.forename: Ao
authors.initials: A
authors.lastname: Ma
mesh_terms: D000409:Alanine / Q000737:chemistry*; D002623:Chemistry Techniques, Analytical / Q000191:economics*; D003198:Computer Simulation / Q000191:economics*; D004151:Dipeptides / Q000737:chemistry*
chemical_list: D004151:Dipeptides; D000409:Alanine