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Hierarchical atom type definitions and extensible all‐atom force fields
Author(s) -
Jin Zhao,
Yang Chunwei,
Cao Fenglei,
Li Feng,
Jing Zhifeng,
Chen Long,
Shen Zhe,
Xin Liang,
Tong Sijia,
Sun Huai
Publication year - 2016
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24244
Subject(s) - parameterized complexity , force field (fiction) , extensibility , atom (system on chip) , scaling , london dispersion force , field (mathematics) , statistical physics , type (biology) , molecule , computer science , chemical physics , computational chemistry , chemistry , physics , quantum mechanics , algorithm , mathematics , geometry , van der waals force , pure mathematics , operating system , ecology , biology , embedded system
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.