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

Ernesto Suarez, Steven Lettieri, Matthew C. Zwier, Carsen A. Stringer, Sundar Raman Subramanian, Lillian T. Chong, Daniel M. Zuckerman
2014 arXiv   pre-print
Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many non-equilibrium 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] to generate equilibrium trajectory ensembles and extract non-equilibrium subsets for computing kinetic quantities. States do not need to be chosen in
more » ... . 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 non-equilibrium observables when phase space has been divided into arbitrary non-Markovian regions, whether in WE or ordinary simulation. In this proof-of-principle study, these methods are successfully applied and validated on two molecular systems: explicitly solvated methane association and the implicitly solvated Ala4 peptide. We comment on challenges remaining in WE calculations.
arXiv:1210.3094v2 fatcat:k32g2nojwncspfxy2or4xxoxw4