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Equilibrium formally can be represented as an ensemble of uncoupled systemsundergoing unbiased dynamics in which detailed balance is maintained. Manynon-equilibrium processes can be described by suitable subsets of theequilibrium ensemble. Here, we employ the "weighted ensemble" (WE) simulationprotocol [Huber and Kim, Biophys. J., 1996] to generate equilibrium trajectoryensembles and extract non-equilibrium subsets for computing kinetic quantities.States do not need to be chosen in advance. The procedure formally allowsestimation of kinetic rates between arbitrary states chosen after thesimulation, along with their equilibrium populations. We also describe arelated history-dependent matrix procedure for estimating equilibrium andnon-equilibrium observables when phase space has been divided into arbitrarynon-Markovian regions, whether in WE or ordinary simulation. In thisproof-of-principle study, these methods are successfully applied and validatedon two molecular systems: explicitly solvated methane association and theimplicitly solvated Ala4 peptide. We comment on challenges remaining in WEcalculations.

Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories