One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution.
In general, finding a one-dimensional representation of the kinetics of a high-dimensional system is a great simplification for the study of complex systems. Here, we propose a method to obtain a reaction coordinate whose potential of the mean force can reproduce the commitment probability distribution from the multidimensional surface. We prove that such a relevant one-dimensional representation can be readily calculated from the equilibrium distribution of commitment probabilities, which can be obtained with simulations. Also, it is shown that this representation is complementary to a previously proposed one-dimensional representation based on a quadratic approximation of the potential energy surface. The usefulness of the method is examined with dynamics in a two-dimensional system, showing that the one-dimensional surface thus obtained can predict the existence of an intermediate and the occurrence of path switching without a priori knowledge of the morphology of the original surface. The applicability of the method to more complex and realistic reactions such as protein folding is also discussed.
Rhee
Young Min
YM
Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.
Pande
Vijay S
VS