gmx_ffconv：一个快速，用户友好的半自动全原子力场转换器，用于gromac。

IF 5.3 2区化学 Q1 CHEMISTRY, MEDICINAL

Journal of Chemical Information and Modeling Pub Date : 2025-09-20 DOI:10.1021/acs.jcim.5c02200

Jasmine E Aaltonen

{"title":"gmx_ffconv：一个快速，用户友好的半自动全原子力场转换器，用于gromac。","authors":"Jasmine E Aaltonen","doi":"10.1021/acs.jcim.5c02200","DOIUrl":null,"url":null,"abstract":"This application note presents gmx_ffconv, a command-line tool developed to facilitate the conversion of systems between all-atom force fields within GROMACS. As different force fields use their own naming conventions and atom ordering, force field conversion within GROMACS is usually a time-consuming, error-prone process. gmx_ffconv resolves atom ordering and naming mismatches between different force fields by reordering the coordinate file via molecular graph matching. This enables the use of identical starting coordinates across force fields, facilitating comparative simulations without requiring manual reordering or scripting. The tool has been validated on a broad range of systems, from small, nonstandard ligands to large, solvated heterogeneous systems with more than two million atoms. gmx_ffconv is available on GitHub: github.com/Jassu1998/gmx_ffconv.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"85 1","pages":""},"PeriodicalIF":5.3000,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS.\",\"authors\":\"Jasmine E Aaltonen\",\"doi\":\"10.1021/acs.jcim.5c02200\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"This application note presents gmx_ffconv, a command-line tool developed to facilitate the conversion of systems between all-atom force fields within GROMACS. As different force fields use their own naming conventions and atom ordering, force field conversion within GROMACS is usually a time-consuming, error-prone process. gmx_ffconv resolves atom ordering and naming mismatches between different force fields by reordering the coordinate file via molecular graph matching. This enables the use of identical starting coordinates across force fields, facilitating comparative simulations without requiring manual reordering or scripting. The tool has been validated on a broad range of systems, from small, nonstandard ligands to large, solvated heterogeneous systems with more than two million atoms. gmx_ffconv is available on GitHub: github.com/Jassu1998/gmx_ffconv.\",\"PeriodicalId\":44,\"journal\":{\"name\":\"Journal of Chemical Information and Modeling \",\"volume\":\"85 1\",\"pages\":\"\"},\"PeriodicalIF\":5.3000,\"publicationDate\":\"2025-09-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Information and Modeling \",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jcim.5c02200\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MEDICINAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.5c02200","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}

引用次数: 0

摘要

本应用笔记介绍了gmx_ffconv，这是一个命令行工具，用于促进GROMACS中全原子力场之间的系统转换。由于不同的力场使用自己的命名约定和原子顺序，因此GROMACS中的力场转换通常是一个耗时且容易出错的过程。Gmx_ffconv通过分子图匹配对坐标文件重新排序，解决了不同力场之间的原子排序和命名不匹配问题。这使得在力场中使用相同的起始坐标，便于比较模拟，而无需手动重新排序或编写脚本。该工具已在广泛的系统中得到验证，从小型非标准配体到大型溶剂化非均匀系统，超过200万个原子。gmx_ffconv可在GitHub: github.com/Jassu1998/gmx_ffconv。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS.

This application note presents gmx_ffconv, a command-line tool developed to facilitate the conversion of systems between all-atom force fields within GROMACS. As different force fields use their own naming conventions and atom ordering, force field conversion within GROMACS is usually a time-consuming, error-prone process. gmx_ffconv resolves atom ordering and naming mismatches between different force fields by reordering the coordinate file via molecular graph matching. This enables the use of identical starting coordinates across force fields, facilitating comparative simulations without requiring manual reordering or scripting. The tool has been validated on a broad range of systems, from small, nonstandard ligands to large, solvated heterogeneous systems with more than two million atoms. gmx_ffconv is available on GitHub: github.com/Jassu1998/gmx_ffconv.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Journal of Chemical Information and Modeling 化学-化学综合

CiteScore

9.80

自引率

10.70%

发文量

529

审稿时长

1.4 months

期刊介绍： The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.