charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

Validation dataset for the paper "charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS". The dataset includes molecular dynamics input and output files, as well as scripts for running the simulations and analyzing the results, used for validating the ported CHARMM parameters. CHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation engine of the same name, it is also usable with other codes. GROMACS is a well-established, highly optimized and multi-purpose software for molecular dynamics, versatile enough to accommodate many different force field potential functions and the associated algorithms. Due to conceptional differences related to software design and the large amount of numeric data inherent to residue topologies and parameter sets, conversion from one software format to another is not straightforward. Here, we present an automated and validated means to port the CHARMM force field to a format read by the GROMACS engine, harmonizing the different capabilities of the two codes in a self-documenting and reproducible way, with a bare minimum of user interaction required. Being based entirely on the upstream data files, the presented approach does not involve any hard-wired/boilerplate code, in contrast with previous attempts to solve the same problem. The heuristic approach used for perceiving local internal geometry is directly applicable for analogous transformations of other force fields.论文《charmm2gmx：将CHARMM加性力场移植至GROMACS的自动化方法》配套的验证数据集。本数据集包含分子动力学输入与输出文件，以及用于运行模拟与结果分析的脚本，用于验证已移植的CHARMM参数。 CHARMM是目前应用最广泛的生物分子力场之一。尽管其开发与同名的专用分子模拟引擎紧密结合，但该力场也可适配其他模拟代码。GROMACS是一款成熟、高度优化且多功能的分子动力学软件，其通用性极强，可兼容多种不同的力场势能函数及配套算法。由于软件设计层面的理念差异，以及残基拓扑结构与参数集本身蕴含的大量数值数据，将力场从一款软件的格式转换至另一款的过程并非易事。 本研究提出了一种自动化且经过验证的方法，可将CHARMM力场转换为GROMACS引擎可读取的格式，以自文档化且可复现的方式协调两款软件的不同功能，同时仅需极少的用户交互操作。该方法完全基于上游数据文件构建，未涉及任何硬编码/样板代码，与此前解决该问题的同类尝试形成鲜明对比。本方法中用于识别局部内部几何结构的启发式策略，可直接推广至其他力场的类似转换任务中。