Reproducible Orchestration of Best Practices for Reaction Path Optimization with the Nudged Elastic Band
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arXiv
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| Format: | Preprint |
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2026
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| _version_ | 1866915939168026624 |
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| author | Goswami, Rohit |
| author_facet | Goswami, Rohit |
| contents | The nudged elastic band (NEB) method is the standard approach for finding minimum energy paths and transition states on potential energy surfaces. Practical NEB calculations require several pre-processing steps: endpoint minimization, structural alignment, and initial path generation. These steps are typically handled by ad-hoc scripts or manual intervention, introducing errors and hindering reproducibility. We present a fully automated, open-source Snakemake workflow for small gas phase molecules that couples modern machine learning potentials (PET-MAD) to the eOn saddle point search software. Each step of the calculation lifecycle is encoded as an explicit dependency graph, from model retrieval and endpoint preparation through path initialization and band optimization. The workflow resolves all software dependencies from conda-forge, ensuring identical execution across platforms. Validation on the HCN to HNC isomerization demonstrates that the automated pipeline recovers the known single-barrier energy profile and product energy without manual intervention. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2603_14737 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Reproducible Orchestration of Best Practices for Reaction Path Optimization with the Nudged Elastic Band Goswami, Rohit Chemical Physics The nudged elastic band (NEB) method is the standard approach for finding minimum energy paths and transition states on potential energy surfaces. Practical NEB calculations require several pre-processing steps: endpoint minimization, structural alignment, and initial path generation. These steps are typically handled by ad-hoc scripts or manual intervention, introducing errors and hindering reproducibility. We present a fully automated, open-source Snakemake workflow for small gas phase molecules that couples modern machine learning potentials (PET-MAD) to the eOn saddle point search software. Each step of the calculation lifecycle is encoded as an explicit dependency graph, from model retrieval and endpoint preparation through path initialization and band optimization. The workflow resolves all software dependencies from conda-forge, ensuring identical execution across platforms. Validation on the HCN to HNC isomerization demonstrates that the automated pipeline recovers the known single-barrier energy profile and product energy without manual intervention. |
| title | Reproducible Orchestration of Best Practices for Reaction Path Optimization with the Nudged Elastic Band |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2603.14737 |