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

Ernesto Suárez, Steven Lettieri, Matthew C. Zwier, Carsen A. Stringer, Sundar Raman Subramanian, Lillian T. Chong, Daniel Zuckerman

Research output: Contribution to journalArticle

29 Citations (Scopus)

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 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.

Original languageEnglish (US)
Pages (from-to)2658-2667
Number of pages10
JournalJournal of Chemical Theory and Computation
Volume10
Issue number7
DOIs
StatePublished - Jul 8 2014
Externally publishedYes

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Trajectories
trajectories
Kinetics
Methane
Peptides
set theory
hubs
simulation
kinetics
peptides
estimating
methane
histories
matrices

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories. / Suárez, Ernesto; Lettieri, Steven; Zwier, Matthew C.; Stringer, Carsen A.; Subramanian, Sundar Raman; Chong, Lillian T.; Zuckerman, Daniel.

In: Journal of Chemical Theory and Computation, Vol. 10, No. 7, 08.07.2014, p. 2658-2667.

Research output: Contribution to journalArticle

Suárez, Ernesto ; Lettieri, Steven ; Zwier, Matthew C. ; Stringer, Carsen A. ; Subramanian, Sundar Raman ; Chong, Lillian T. ; Zuckerman, Daniel. / Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories. In: Journal of Chemical Theory and Computation. 2014 ; Vol. 10, No. 7. pp. 2658-2667.
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