title: Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.
abstract: DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.
authors.affiliation: Scientific Computing Department, Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury , Warrington WA4 4AD, U.K.|Manchester Pharmacy School, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, The University of Manchester , Manchester M13 9NT, U.K.
authors.forename: Chin W
authors.initials: CW
authors.lastname: Yong
mesh_terms: D000069059:Atorvastatin / Q000737:chemistry; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation
chemical_list: D000069059:Atorvastatin