منابع مشابه
Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning
Reaction coordinates are vital tools for qualitative and quantitative analysis of molecular processes. They provide a simple picture of reaction progress and essential input for calculations of free energies and rates. Iso-committor surfaces are considered the optimal reaction coordinate. We present an algorithm to compute efficiently a sequence of isocommittor surfaces. These surfaces are cons...
متن کاملComputing time scales from reaction coordinates by milestoning.
An algorithm is presented to compute time scales of complex processes following predetermined milestones along a reaction coordinate. A non-Markovian hopping mechanism is assumed and constructed from underlying microscopic dynamics. General analytical analysis, a pedagogical example, and numerical solutions of the non-Markovian model are presented. No assumption is made in the theoretical deriv...
متن کاملReaction Path Hamiltonian Based on a Reaction Coordinate and a Curvature Coordinate
We propose a reaction path‐based Hamiltonian in terms of the reaction coordinate, the curvature coordinate, the remaining 3N−8 transverse normal coordinates (whose directions are orthogonal to the path tangent and curvature vectors), and their conjugate momenta, for an Natomic reaction system. The 3N−8 transverse vibrational modes are independent of the motion along the reaction path, although ...
متن کاملA Mathematical Framework for Exact Milestoning
We give a mathematical framework for Exact Milestoning, a recently introduced algorithm for mapping a continuous time stochastic process into a Markov chain or semi-Markov process that can be efficiently simulated and analyzed. We generalize the setting of Exact Milestoning and give explicit error bounds for the error in the Milestoning equation for mean first passage times.
متن کاملAdiabatic invariance along the reaction coordinate.
In a two-dimensional space where a point particle interacts with a diatomic fragment, the action integral contour integral of p(theta) d theta (where theta is the angle between the fragment and the line of centers and p(theta) its conjugate momentum) is an adiabatic invariant. This invariance is thought to be a persistent dynamical constraint. Indeed, its classical Poisson bracket with the Hami...
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ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2010
ISSN: 1549-9618,1549-9626
DOI: 10.1021/ct100114j