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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Bibliographic Details
Published in:Journal of chemical theory and computation Vol. 11; no. 11; p. 5062
Main Authors: Pfaendtner, Jim, Bonomi, Massimiliano
Format: Journal Article
Language:English
Published: United States 10.11.2015
Subjects:
Algorithms
Models, Biological
Molecular Dynamics Simulation
Thermodynamics
Tryptophan - chemistry
ISSN:1549-9626, 1549-9626
Online Access:Get more information
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Summary: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.
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ISSN:1549-9626
1549-9626
DOI:10.1021/acs.jctc.5b00846