Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.

ABSTRACT: Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many nonequilibrium processes can be described by suitable subsets of the equilibrium ensemble. Here, we employ the "weighted ensemble" (WE) simulation protocol [Huber and Kim, Biophys. J.1996, 70, 97-110] to generate equilibrium trajectory ensembles and extract nonequilibrium subsets for computing kinetic quantities. States do not need to be chosen in advance. The procedure formally allows estimation of kinetic rates between arbitrary states chosen after the simulation, along with their equilibrium populations. We also describe a related history-dependent matrix procedure for estimating equilibrium and nonequilibrium observa

SUBMITTER: Suarez E 

PROVIDER: S-EPMC4168800 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature