Hierarchical atom type definitions and extensible all‐atom force fields. Issue 7 (5th November 2015)

• Record Type: Journal Article
• Authors: Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai
• Is Part Of: Journal of computational chemistry. Volume 37:Issue 7(2016)
• Page Start: 653
• Page End: 664
• Publication Date: 2015-11-05
• Subjects: all‐atom force field -- atom types -- extensibility -- hydration free energy -- organic compounds; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.24244
• Languages: English
• ISSNs: 0192-8651

Abstract

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. Abstract : A hierarchical definition of atom type is proposed to solve the problem of "missing parameters". The extensible atom type definitions make the force field extensible. Two general force fields are parameterized for some common organic molecules. Parameters are derived from ab initial data and experimental liquid data. Calculation results show good accuracy of the parameters.