Yong Chin W
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.
J Chem Inf Model. 2016 Aug 22;56(8):1405-9. doi: 10.1021/acs.jcim.6b00323. Epub 2016 Aug 4.
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.
DL_F 符号是一种易于理解的标准化原子排版表达式，用于一系列有机力场（FF）方案（如OPLSAA、PCFF和CVFF）的分子模拟。它在DL_FIELD软件程序中实现，该软件程序有助于为DL_POLY分子动力学模拟软件建立分子FF模型。通过使用该符号，DL_FIELD中实现的单个核心转换模块（DL_F转换引擎）可用于分析分子结构并确定给定FF方案的原子类型。用户只需以简单的xyz格式提供分子输入结构，DL_FIELD就能自动为DL_POLY生成必要的力场文件。与强调稳健性和用户友好性的DL_FIELD开发理念相一致，该引擎为设置复杂的FF模型提供了单步解决方案。这允许用户从上述FF方案之一无缝切换到另一个方案，同时提供以自然化学意义表示的一致原子类型。
