### Abstract

In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of "chromosomes" which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/ extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set, as indicated by the reduction in errors of the calculated pure liquid densities (d), heats of vaporization (H _{vap}), and hydration energies. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of H _{vap} was reduced from 1.98 to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable performance was observed when the optimized vdW set was combined with the Thole Amoeba-like polarizable model, particularly for the interaction energy and liquid density calculations. Thus, the optimized vdW set is applicable to both types of Thole models with either linear or Amoeba-like screening functions.

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

Pages (from-to) | 7088-7101 |

Number of pages | 14 |

Journal | Journal of Physical Chemistry B |

Volume | 116 |

Issue number | 24 |

DOIs | |

State | Published - Jun 21 2012 |

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### ASJC Scopus subject areas

- Physical and Theoretical Chemistry
- Materials Chemistry
- Surfaces, Coatings and Films

### Cite this

*Journal of Physical Chemistry B*,

*116*(24), 7088-7101. https://doi.org/10.1021/jp3019759

**Development of polarizable models for molecular mechanical calculations. 4. van der waals parametrization.** / Wang, Junmei; Cieplak, Piotr; Li, Jie; Cai, Qin; Hsieh, Meng Juei; Luo, Ray; Duan, Yong.

Research output: Contribution to journal › Article

*Journal of Physical Chemistry B*, vol. 116, no. 24, pp. 7088-7101. https://doi.org/10.1021/jp3019759

}

TY - JOUR

T1 - Development of polarizable models for molecular mechanical calculations. 4. van der waals parametrization

AU - Wang, Junmei

AU - Cieplak, Piotr

AU - Li, Jie

AU - Cai, Qin

AU - Hsieh, Meng Juei

AU - Luo, Ray

AU - Duan, Yong

PY - 2012/6/21

Y1 - 2012/6/21

N2 - In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of "chromosomes" which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/ extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set, as indicated by the reduction in errors of the calculated pure liquid densities (d), heats of vaporization (H vap), and hydration energies. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of H vap was reduced from 1.98 to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable performance was observed when the optimized vdW set was combined with the Thole Amoeba-like polarizable model, particularly for the interaction energy and liquid density calculations. Thus, the optimized vdW set is applicable to both types of Thole models with either linear or Amoeba-like screening functions.

AB - In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of "chromosomes" which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/ extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set, as indicated by the reduction in errors of the calculated pure liquid densities (d), heats of vaporization (H vap), and hydration energies. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of H vap was reduced from 1.98 to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable performance was observed when the optimized vdW set was combined with the Thole Amoeba-like polarizable model, particularly for the interaction energy and liquid density calculations. Thus, the optimized vdW set is applicable to both types of Thole models with either linear or Amoeba-like screening functions.

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UR - http://www.scopus.com/inward/citedby.url?scp=84862654593&partnerID=8YFLogxK

U2 - 10.1021/jp3019759

DO - 10.1021/jp3019759

M3 - Article

C2 - 22612331

AN - SCOPUS:84862654593

VL - 116

SP - 7088

EP - 7101

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 24

ER -