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Verfasst von:Prinz, Jan-Hendrik [VerfasserIn]   i
 Chodera, John D. [VerfasserIn]   i
 Pande, Vijay S. [VerfasserIn]   i
 Swope, William C. [VerfasserIn]   i
 Smith, Jeremy C. [VerfasserIn]   i
 Noé, Frank [VerfasserIn]   i
Titel:Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics
Verf.angabe:Jan-Hendrik Prinz, John D. Chodera, Vijay S. Pande, William C. Swope, Jeremy C. Smith, and Frank Noé
E-Jahr:2011
Jahr:24 June 2011
Umfang:14 S.
Fussnoten:Gesehen am 17.01.2023
Titel Quelle:Enthalten in: The journal of chemical physics
Ort Quelle:Melville, NY : American Institute of Physics, 1933
Jahr Quelle:2011
Band/Heft Quelle:134(2011), 24, Artikel-ID 244108, Seite 1-14
ISSN Quelle:1089-7690
Abstract:Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.
DOI:doi:10.1063/1.3592153
URL:Bitte beachten Sie: Dies ist ein Bibliographieeintrag. Ein Volltextzugriff für Mitglieder der Universität besteht hier nur, falls für die entsprechende Zeitschrift/den entsprechenden Sammelband ein Abonnement besteht oder es sich um einen OpenAccess-Titel handelt.

Volltext: https://doi.org/10.1063/1.3592153
 Volltext: https://aip.scitation.org/doi/10.1063/1.3592153
 DOI: https://doi.org/10.1063/1.3592153
Datenträger:Online-Ressource
Sprache:eng
K10plus-PPN:1831246619
Verknüpfungen:→ Zeitschrift

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