title: Revisiting and computing reaction coordinates with Directional Milestoning.
abstract: The method of Directional Milestoning is revisited. We start from an exact and more general expression and state the conditions and validity of the memory-loss approximation. An algorithm to compute a reaction coordinate from Directional Milestoning data is presented. The reaction coordinate is calculated as a set of discrete jumps between Milestones that maximizes the flux between two stable states. As an application we consider a conformational transition in solvated adenosine. We compare a long molecular dynamic trajectory with Directional Milestoning and discuss the differences between the maximum flux path and minimum energy coordinates.
authors.affiliation: Department of Chemistry and Biochemistry, Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
authors.forename: Serdal
authors.initials: S
authors.lastname: Kirmizialtin
authors.forename: Ron
authors.initials: R
authors.lastname: Elber
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation