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

التفاصيل البيبلوغرافية
العنوان: Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.
المؤلفون: Suárez E; Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States., Lettieri S; Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States., Zwier MC; Department of Chemistry, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States., Stringer CA; Gatsby Computational Neuroscience Unit, University College London , Gower St, London WC1E 6BT, United Kingdom., Subramanian SR; Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States., Chong LT; Department of Chemistry, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States., Zuckerman DM; Department of Computational and Systems Biology, University of Pittsburgh , 4200 Fifth Ave, Pittsburgh, Pennsylvania 15260, United States.
المصدر: Journal of chemical theory and computation [J Chem Theory Comput] 2014 Jul 08; Vol. 10 (7), pp. 2658-2667. Date of Electronic Publication: 2014 Mar 03.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: Washington, D.C. : American Chemical Society, c2005-
مستخلص: 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.
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معلومات مُعتمدة: P41 GM103712 United States GM NIGMS NIH HHS
تواريخ الأحداث: Date Created: 20140924 Latest Revision: 20211021
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC4168800
DOI: 10.1021/ct401065r
PMID: 25246856
قاعدة البيانات: MEDLINE
الوصف
تدمد:1549-9626
DOI:10.1021/ct401065r