title: Hierarchical atom type definitions and extensible all-atom force fields.
abstract: The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc.
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Jin
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Chunwei
authors.initials: C
authors.lastname: Yang
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Fenglei
authors.initials: F
authors.lastname: Cao
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Zhifeng
authors.initials: Z
authors.lastname: Jing
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Long
authors.initials: L
authors.lastname: Chen
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Shen
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Xin
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Sijia
authors.initials: S
authors.lastname: Tong
authors.affiliation: School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
authors.forename: Huai
authors.initials: H
authors.lastname: Sun
mesh_terms: D003198:Computer Simulation; D009930:Organic Chemicals / Q000737:chemistry*
chemical_list: D009930:Organic Chemicals
keywords: all-atom force field; atom types; extensibility; hydration free energy; organic compounds