### Abstract

The efficient and reliable computation of relative free energy changes for alchemical mutation is very important in biomolecular simulations. In this study we examine the utility of computing alchemical free energy changes using overlap perturbation techniques. These techniques include both the overlap histogram method and the overlap sampling method (a fully optimized version of the overlap sampling technique is equivalent to Bennett's method), and commonly combine sets of perturbations from both alchemical states of interest to improve a free energy calculation. In addition, we propose new variants, present generalized formulas for overlap perturbation techniques and demonstrate differences from the prevailing direct averaging approach used in alchemical free energy calculations. These overlap perturbation methods can be applied to either equilibrium or non-equilibrium free energy simulations. The alchemical transformation of an adenosine molecule in aqueous solution is used as an example for evaluating these techniques. The calculations show that the methods are capable of producing excellent free energy estimates for an extended range of perturbation magnitudes. We suggest that these overlap perturbation methods should be more widely used for the computation of alchemical free energy changes in biomolecular simulations.

Original language | English (US) |
---|---|

Pages (from-to) | 173-181 |

Number of pages | 9 |

Journal | Molecular Physics |

Volume | 102 |

Issue number | 2 PART I |

DOIs | |

State | Published - Jan 20 2004 |

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### ASJC Scopus subject areas

- Atomic and Molecular Physics, and Optics

### Cite this

**Overlap perturbation methods for computing alchemical free energy changes : Variants, generalizations and evaluations.** / Lu, Nandou; Woolf, Thomas B.

Research output: Contribution to journal › Article

*Molecular Physics*, vol. 102, no. 2 PART I, pp. 173-181. https://doi.org/10.1080/00268970310001644603

}

TY - JOUR

T1 - Overlap perturbation methods for computing alchemical free energy changes

T2 - Variants, generalizations and evaluations

AU - Lu, Nandou

AU - Woolf, Thomas B

PY - 2004/1/20

Y1 - 2004/1/20

N2 - The efficient and reliable computation of relative free energy changes for alchemical mutation is very important in biomolecular simulations. In this study we examine the utility of computing alchemical free energy changes using overlap perturbation techniques. These techniques include both the overlap histogram method and the overlap sampling method (a fully optimized version of the overlap sampling technique is equivalent to Bennett's method), and commonly combine sets of perturbations from both alchemical states of interest to improve a free energy calculation. In addition, we propose new variants, present generalized formulas for overlap perturbation techniques and demonstrate differences from the prevailing direct averaging approach used in alchemical free energy calculations. These overlap perturbation methods can be applied to either equilibrium or non-equilibrium free energy simulations. The alchemical transformation of an adenosine molecule in aqueous solution is used as an example for evaluating these techniques. The calculations show that the methods are capable of producing excellent free energy estimates for an extended range of perturbation magnitudes. We suggest that these overlap perturbation methods should be more widely used for the computation of alchemical free energy changes in biomolecular simulations.

AB - The efficient and reliable computation of relative free energy changes for alchemical mutation is very important in biomolecular simulations. In this study we examine the utility of computing alchemical free energy changes using overlap perturbation techniques. These techniques include both the overlap histogram method and the overlap sampling method (a fully optimized version of the overlap sampling technique is equivalent to Bennett's method), and commonly combine sets of perturbations from both alchemical states of interest to improve a free energy calculation. In addition, we propose new variants, present generalized formulas for overlap perturbation techniques and demonstrate differences from the prevailing direct averaging approach used in alchemical free energy calculations. These overlap perturbation methods can be applied to either equilibrium or non-equilibrium free energy simulations. The alchemical transformation of an adenosine molecule in aqueous solution is used as an example for evaluating these techniques. The calculations show that the methods are capable of producing excellent free energy estimates for an extended range of perturbation magnitudes. We suggest that these overlap perturbation methods should be more widely used for the computation of alchemical free energy changes in biomolecular simulations.

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U2 - 10.1080/00268970310001644603

DO - 10.1080/00268970310001644603

M3 - Article

AN - SCOPUS:3042801976

VL - 102

SP - 173

EP - 181

JO - Molecular Physics

JF - Molecular Physics

SN - 0026-8976

IS - 2 PART I

ER -