Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

Metadynamics accelerates sampling of molecular dynamics while reconstructing thermodynamic properties of selected descriptors of the system. Its main practical difficulty originates from the compromise between keeping the number of descriptors small for efficiently exploring their multidimensional f...

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Vydané v:Journal of chemical theory and computation Ročník 11; číslo 11; s. 5062
Hlavní autori: Pfaendtner, Jim, Bonomi, Massimiliano
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States 10.11.2015
Predmet:
Algorithms
Models, Biological
Molecular Dynamics Simulation
Thermodynamics
Tryptophan - chemistry
ISSN:1549-9626, 1549-9626
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Shrnutí:Metadynamics accelerates sampling of molecular dynamics while reconstructing thermodynamic properties of selected descriptors of the system. Its main practical difficulty originates from the compromise between keeping the number of descriptors small for efficiently exploring their multidimensional free-energy landscape and biasing all of the slow motions of a process. Here we illustrate on a model system and on the tryptophan-cage miniprotein parallel bias metadynamics, a method that overcomes this issue by simultaneously applying multiple low-dimensional bias potentials.
Bibliografia:ObjectType-Article-1
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content type line 23
ISSN:1549-9626
1549-9626
DOI:10.1021/acs.jctc.5b00846