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Cited by 615

The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.

Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics

Raiteri, Paolo, Laio, Alessandro, Gervasio, Francesco Luigi, Micheletti, Cristian, Parrinello, Michele·2006·The Journal of Physical Chemistry B
DOI 10.1021/jp054359r
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Abstract

Recently, we have introduced a new method, metadynamics, which is able to sample rarely occurring transitions and to reconstruct the free energy as a function of several variables with a controlled accuracy. This method has been successfully applied in many different fields, ranging from chemistry to biophysics and ligand docking and from material science to crystal structure prediction. We present an important development that speeds up metadynamics calculations by orders of magnitude and renders the algorithm much more robust. We use multiple interacting simulations, walkers, for exploring and reconstructing the same free energy surface. Each walker contributes to the history-dependent potential that, in metadynamics, is an estimate of the free energy. We show that the error on the reconstructed free energy does not depend on the number of walkers, leading to a fully linear scaling algorithm even on inexpensive loosely coupled clusters of PCs. In addition, we show that the accuracy and stability of the method are much improved by combining it with a weighted histogram analysis. We check the validity of our new method on a realistic application.

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Metadata

Authors
Raiteri, P., Laio, A., Gervasio, F. L., Micheletti, C., & Parrinello, M.
Venue
The Journal of Physical Chemistry B
Publisher
American Chemical Society (ACS)
Published
2005-10-28
Volume
110
Issue
8
Pages
3533-3539
ISSN
  • 1520-5207 (ISSN-L)
  • 1520-6106
DOI
10.1021/jp054359r
OpenAlex
W2029186981
Cited by
615
References
40
FWCI
5.60
Type
journal article
Language
en
Open access
closed

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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

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