Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern, 67663, Germany.
Sci Data. 2023 Jul 27;10(1):495. doi: 10.1038/s41597-023-02369-8.
A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format is machine readable, re-usable, and interoperable. A transferable force field is a chemical construction plan specifying intermolecular and intramolecular interactions between different types of atoms or different chemical groups and can be used for building a model for a given component. The data scheme proposed in this work (named TUK-FFDat) formalizes digitally these chemical construction plans, i.e. transferable force fields. It can be applied to all-atom as well as united-atom transferable force fields. The general applicability of the data scheme is demonstrated for different types of force fields (TraPPE, OPLS-AA, and Potoff). Furthermore, conversion tools for translating the data scheme between .xls spread sheet format and the SQL-based data format are provided. The data format can readily be integrated in existing workflows, simulation engines, and force field databases as well as for linking such.
提出了一种用于分子模拟（即分子动力学和蒙特卡罗模拟）的可转移经典力场的通用数据方案。该数据方案以基于 SQL 的数据格式实现。该数据方案和数据格式是机器可读、可重复使用和可互操作的。可转移力场是指定不同类型的原子或不同化学基团之间的分子间和分子内相互作用的化学结构计划，可用于为给定组件构建模型。本工作中提出的数据方案（命名为 TUK-FFDat）以数字方式形式化了这些化学结构计划，即可转移力场。它可以应用于全原子和统一原子的可转移力场。该数据方案的通用性通过不同类型的力场（TraPPE、OPLS-AA 和 Potoff）得到了证明。此外，还提供了用于在.xls 电子表格格式和基于 SQL 的数据格式之间转换数据方案的转换工具。该数据格式可以轻松集成到现有的工作流程、模拟引擎和力场数据库中，以及用于链接这些。
