Paper Citing NAMD - Abstract
Dixit, Purushottam D.; Dill, Ken A.
Inferring Microscopic Kinetic Rates from Stationary State Distributions
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3002-3005, AUG 2014
We present a principled approach for estimating the matrix of microscopic transition probabilities among states of a Markov process, given only its stationary state population distribution and a single average global kinetic observable. We adapt Maximum Caliber, a variational principle in which the path entropy is maximized over the distribution of all possible trajectories, subject to basic kinetic constraints and some average dynamical observables. We illustrate the method by computing the solvation dynamics of water molecules from molecular dynamics trajectories.
