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  Kinetics from Replica Exchange Molecular Dynamics Simulations

Stelzl, L. S., & Hummer, G. (2017). Kinetics from Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 13(8), 3927-3935. doi:10.1021/acs.jctc.7b00372.

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 Creators:
Stelzl, Lukas S.1, Author           
Hummer, Gerhard1, Author                 
Affiliations:
1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              

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 Abstract: Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

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Language(s): eng - English
 Dates: 2017-04-072017-06-282017-08-08
 Publication Status: Published in print
 Pages: 9
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jctc.7b00372
 Degree: -

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Title: Journal of Chemical Theory and Computation
  Other : J. Chem. Theory Comput.
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 13 (8) Sequence Number: - Start / End Page: 3927 - 3935 Identifier: Other: 1549-9618
CoNE: https://pure.mpg.de/cone/journals/resource/111088195283832