dmf-g16: A Gaussian Wrapper for Reliable Double-Ended Transition-State Searches With Native Input Formats.

IF 4.8 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY
Shin-Ichi Koda, Shinji Saito
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引用次数: 0

Abstract

Transition-state (TS) searches are central to computational studies of chemical reactions, yet advanced methods often require substantial effort to integrate into routine workflows. Consequently, users tend to rely on familiar software and established input formats. Here, we present dmf-g16, a Gaussian-specific front end to the Direct MaxFlux (DMF) reaction-path optimization method implemented in PyDMF. dmf-g16 enables DMF-based TS searches with minimal workflow changes: users simply replace the Gaussian executable with dmf-g16, while native QST2/QST3 input files remain unchanged. For QST inputs, DMF performs explicit path optimization using Gaussian as an external energy calculator, followed by TS refinement in Gaussian from the highest-energy path point. Benchmarks on 121 reactions show a substantial improvement in reliability over Gaussian QST2, increasing the success rate from 31.4% to 93.4%. Although path optimization adds computational cost, wall-clock time is typically only a few times that of QST2 and can be reduced through parallel energy evaluation.

dmf-g16:使用本地输入格式进行可靠的双端过渡状态搜索的高斯包装器。
过渡状态(TS)搜索是化学反应计算研究的核心,然而先进的方法通常需要大量的努力才能集成到日常工作流程中。因此,用户倾向于依赖熟悉的软件和既定的输入格式。在这里,我们提出了DMF -g16,这是在PyDMF中实现的直接MaxFlux (DMF)反应路径优化方法的高斯特定前端。dmf-g16使基于dmf的TS搜索与最小的工作流程变化:用户只需用dmf-g16替换高斯可执行文件,而本地QST2/QST3输入文件保持不变。对于QST输入,DMF使用高斯作为外部能量计算器执行显式路径优化,然后从能量最高的路径点开始在高斯中进行TS细化。121个反应的基准测试表明,与高斯QST2相比,可靠性有了实质性的提高,成功率从31.4%提高到93.4%。虽然路径优化增加了计算成本,但挂钟时间通常只有QST2的几倍,并且可以通过并行能量评估来减少挂钟时间。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
6.60
自引率
3.30%
发文量
247
审稿时长
1.7 months
期刊介绍: This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.
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