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Cited by 871

The DOI matches its Crossref record; 53 of the 53 references it cites were found in a registry or an index.

Adaptive biasing force method for scalar and vector free energy calculations

Darve, Eric, Rodríguez-Gómez, David, Pohorille, Andrew·2008·The Journal of Chemical Physics
DOI 10.1063/1.2829861
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Abstract

In free energy calculations based on thermodynamic integration, it is necessary to compute the derivatives of the free energy as a function of one (scalar case) or several (vector case) order parameters. We derive in a compact way a general formulation for evaluating these derivatives as the average of a mean force acting on the order parameters, which involves first derivatives with respect to both Cartesian coordinates and time. This is in contrast with the previously derived formulas, which require first and second derivatives of the order parameter with respect to Cartesian coordinates. As illustrated in a concrete example, the main advantage of this new formulation is the simplicity of its use, especially for complicated order parameters. It is also straightforward to implement in a molecular dynamics code, as can be seen from the pseudocode given at the end. We further discuss how the approach based on time derivatives can be combined with the adaptive biasing force method, an enhanced sampling technique that rapidly yields uniform sampling of the order parameters, and by doing so greatly improves the efficiency of free energy calculations. Using the backbone dihedral angles Φ and Ψ in N-acetylalanyl-N′-methylamide as a numerical example, we present a technique to reconstruct the free energy from its derivatives, a calculation that presents some difficulties in the vector case because of the statistical errors affecting the derivatives.

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Metadata

Authors
Darve, E., Rodríguez-Gómez, D., & Pohorille, A.
Venue
The Journal of Chemical Physics
Publisher
AIP Publishing
Published
2008-04-11
Volume
128
Issue
14
Pages
144120-144120
ISSN
  • 0021-9606 (ISSN-L)
  • 1089-7690
DOI
10.1063/1.2829861
OpenAlex
W2042821667
Cited by
871
References
53
FWCI
5.09
Type
journal article
Language
en
Open access
closed

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