Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations
Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations
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DOI：
10.1021/acs.jcim.6b00323
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发表时间：
2016-08-01
影响因子：
5.6
通讯作者：
Yong, Chin W.
中科院分区：
文献类型：
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作者：
Yong, Chin W.
DL_F表示法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)方案的分子模拟，如OPLSAA、PCFF和CVFF。它是在DL_FIELD中实现的，这是一个为DL_Poly分子动力学模拟软件建立分子FF模型的软件程序。通过使用该符号，可以使用在DL_FIELD内实现的单个核心转换模块(DL_F转换引擎)来分析分子结构并确定给定的FF方案的原子类型。用户只需要提供简单的XYZ格式的分子输入结构，DL_FIELD就可以自动生成DL_POLY所需的力场文件。与强调健壮性和用户友好性的DL_FIELD的开发理念相适应，该引擎为设置复杂的FF模型提供了一步解决方案。这允许用户从上述FF中的一种无缝切换到另一种，同时提供以自然化学意义表示的一致的原子分型。
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.