Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

By Cameron F. Abrams, Giovanni Bussi. Entropy, 2013

405 citations recorded by the source corpus.

We review a selection of methods for performing enhanced sampling in 1 molecular dynamics simulations. We consider methods based on collective variable biasing 2

Subfields: Atomic and Molecular Physics, and Optics, Condensed Matter Physics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/460bb24c9c7bb1594049fecb52f906f458cc8bef

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In Atomic and Molecular Physics, and Optics

In Condensed Matter Physics

In Molecular Biology

Citations in the corpus

Experimental accuracy in protein structure refinement via molecular dynamics simulations (2018, background): “In principle, enhanced sampling techniques (54) could be applied to specific barriers, e.”
Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “150 In protein folding simulations, enhanced sampling techniques can accelerate in silico folding by several orders of magnitude.”
Unsupervised Learning Methods for Molecular Simulation Data (2021, neutral): “233,234 5.”
Martini straight: Boosting performance using a shorter cutoff and GPUs (2016, methodology): “Several methods to increase the sampling are available, among which the use of designated hardware [2], distributed sampling [3], enhanced sampling methods [4] and the use of coarse grain (CG) models [5].”