### Abstract

A few recent techniques to calculate free energies in the context of molecular dynamics simulations are discussed: temperature-accelerated molecular dynamics, which is a method, to explore fast the important regions in the free energy landscape associated with a set of continuous collective variables without having to know where these regions are beforehand; the single sweep method, which is a variational method to interpolate the free energy globally given a set of mean forces (i.e., a set of gradients of the free energy) calculated at specific points, or centers, on the free energy landscape; and a Voronoi-based free energy method, for the calculation of the free energy of the Voronoi tessellation associated with a set of centers. We also discuss how this last technique can be used, in conjunction with the string method, and how kinetic information such as reaction rates can be calculated by milestoning using the edges of a Voronoi tessellation as milestones.

Original language | English (US) |
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Pages (from-to) | 1737-1747 |

Number of pages | 11 |

Journal | Journal of Computational Chemistry |

Volume | 30 |

Issue number | 11 |

DOIs | |

State | Published - Aug 2009 |

### Fingerprint

### Keywords

- Free energy
- Markov state model
- Milestoning
- Single sweep
- String method
- Temperature accelerated
- Voronoi tessellation

### ASJC Scopus subject areas

- Chemistry(all)
- Computational Mathematics

### Cite this

**Some recent techniques for free energy calculations.** / Vanden Eijnden, Eric.

Research output: Contribution to journal › Article

*Journal of Computational Chemistry*, vol. 30, no. 11, pp. 1737-1747. https://doi.org/10.1002/jcc.21332

}

TY - JOUR

T1 - Some recent techniques for free energy calculations

AU - Vanden Eijnden, Eric

PY - 2009/8

Y1 - 2009/8

N2 - A few recent techniques to calculate free energies in the context of molecular dynamics simulations are discussed: temperature-accelerated molecular dynamics, which is a method, to explore fast the important regions in the free energy landscape associated with a set of continuous collective variables without having to know where these regions are beforehand; the single sweep method, which is a variational method to interpolate the free energy globally given a set of mean forces (i.e., a set of gradients of the free energy) calculated at specific points, or centers, on the free energy landscape; and a Voronoi-based free energy method, for the calculation of the free energy of the Voronoi tessellation associated with a set of centers. We also discuss how this last technique can be used, in conjunction with the string method, and how kinetic information such as reaction rates can be calculated by milestoning using the edges of a Voronoi tessellation as milestones.

AB - A few recent techniques to calculate free energies in the context of molecular dynamics simulations are discussed: temperature-accelerated molecular dynamics, which is a method, to explore fast the important regions in the free energy landscape associated with a set of continuous collective variables without having to know where these regions are beforehand; the single sweep method, which is a variational method to interpolate the free energy globally given a set of mean forces (i.e., a set of gradients of the free energy) calculated at specific points, or centers, on the free energy landscape; and a Voronoi-based free energy method, for the calculation of the free energy of the Voronoi tessellation associated with a set of centers. We also discuss how this last technique can be used, in conjunction with the string method, and how kinetic information such as reaction rates can be calculated by milestoning using the edges of a Voronoi tessellation as milestones.

KW - Free energy

KW - Markov state model

KW - Milestoning

KW - Single sweep

KW - String method

KW - Temperature accelerated

KW - Voronoi tessellation

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UR - http://www.scopus.com/inward/citedby.url?scp=67650485755&partnerID=8YFLogxK

U2 - 10.1002/jcc.21332

DO - 10.1002/jcc.21332

M3 - Article

VL - 30

SP - 1737

EP - 1747

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 11

ER -