### Resumen

Calculating transition rates and other kinetic quantities from molecular simulations requires knowledge not only of the free energy along the relevant coordinate but also the diffusivity as a function of that coordinate. A variety of methods are currently used to map the free-energy landscape in molecular simulations; however, simultaneous calculation of position-dependent diffusivity is complicated by biasing forces applied with many of these methods. Here, we describe a method to calculate position-dependent diffusivities in simulations including known time-dependent biasing forces, which relies on a previously proposed Bayesian inference scheme. We first apply the method to an explicitly diffusive model, and then to an equilibrium molecular dynamics simulation of liquid water including a position-dependent thermostat, comparing the results to those of an established method. Finally, we test the method on a system of liquid water, where oscillations of the free energy along the coordinate of interest preclude sufficient sampling in an equilibrium simulation. The adaptive biasing force method permits roughly uniform sampling along this coordinate, while the method presented here gives a consistent result for the position-dependent diffusivity, even in a short simulation where the adaptive biasing force is only partially converged.

Idioma original | English |
---|---|

Páginas (desde-hasta) | 876-882 |

Número de páginas | 7 |

Publicación | Journal of Chemical Theory and Computation |

Volumen | 9 |

N.º | 2 |

DOI | |

Estado | Published - 12 feb 2013 |

### Huella dactilar

### ASJC Scopus subject areas

- Computer Science Applications
- Physical and Theoretical Chemistry

### Citar esto

*Journal of Chemical Theory and Computation*,

*9*(2), 876-882. https://doi.org/10.1021/ct300867e

}

*Journal of Chemical Theory and Computation*, vol. 9, n.º 2, pp. 876-882. https://doi.org/10.1021/ct300867e

**Calculating position-dependent diffusivity in biased molecular dynamics simulations.** / Comer, Jeffrey; Chipot, Christophe; González-Nilo, Fernando D.

Resultado de la investigación: Article

TY - JOUR

T1 - Calculating position-dependent diffusivity in biased molecular dynamics simulations

AU - Comer, Jeffrey

AU - Chipot, Christophe

AU - González-Nilo, Fernando D.

PY - 2013/2/12

Y1 - 2013/2/12

N2 - Calculating transition rates and other kinetic quantities from molecular simulations requires knowledge not only of the free energy along the relevant coordinate but also the diffusivity as a function of that coordinate. A variety of methods are currently used to map the free-energy landscape in molecular simulations; however, simultaneous calculation of position-dependent diffusivity is complicated by biasing forces applied with many of these methods. Here, we describe a method to calculate position-dependent diffusivities in simulations including known time-dependent biasing forces, which relies on a previously proposed Bayesian inference scheme. We first apply the method to an explicitly diffusive model, and then to an equilibrium molecular dynamics simulation of liquid water including a position-dependent thermostat, comparing the results to those of an established method. Finally, we test the method on a system of liquid water, where oscillations of the free energy along the coordinate of interest preclude sufficient sampling in an equilibrium simulation. The adaptive biasing force method permits roughly uniform sampling along this coordinate, while the method presented here gives a consistent result for the position-dependent diffusivity, even in a short simulation where the adaptive biasing force is only partially converged.

AB - Calculating transition rates and other kinetic quantities from molecular simulations requires knowledge not only of the free energy along the relevant coordinate but also the diffusivity as a function of that coordinate. A variety of methods are currently used to map the free-energy landscape in molecular simulations; however, simultaneous calculation of position-dependent diffusivity is complicated by biasing forces applied with many of these methods. Here, we describe a method to calculate position-dependent diffusivities in simulations including known time-dependent biasing forces, which relies on a previously proposed Bayesian inference scheme. We first apply the method to an explicitly diffusive model, and then to an equilibrium molecular dynamics simulation of liquid water including a position-dependent thermostat, comparing the results to those of an established method. Finally, we test the method on a system of liquid water, where oscillations of the free energy along the coordinate of interest preclude sufficient sampling in an equilibrium simulation. The adaptive biasing force method permits roughly uniform sampling along this coordinate, while the method presented here gives a consistent result for the position-dependent diffusivity, even in a short simulation where the adaptive biasing force is only partially converged.

UR - http://www.scopus.com/inward/record.url?scp=84873665160&partnerID=8YFLogxK

U2 - 10.1021/ct300867e

DO - 10.1021/ct300867e

M3 - Article

AN - SCOPUS:84873665160

VL - 9

SP - 876

EP - 882

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 2

ER -