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| Autores principales: | , , , |
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| Formato: | Preprint |
| Publicado: |
2024
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| Materias: | |
| Acceso en línea: | https://arxiv.org/abs/2404.02597 |
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| _version_ | 1866916191140839424 |
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| author | Zhang, Jintu Zhang, Odin Bonati, Luigi Hou, TingJun |
| author_facet | Zhang, Jintu Zhang, Odin Bonati, Luigi Hou, TingJun |
| contents | Rare event sampling is a central problem in modern computational chemistry research. Among the existing methods, transition path sampling (TPS) can generate unbiased representations of reaction processes. However, its efficiency depends on the ability to generate reactive trial paths, which in turn depends on the quality of the shooting algorithm used. We propose a new algorithm based on the shooting success rate, i.e. reactivity, measured as a function of a reduced set of collective variables (CVs). These variables are extracted with a machine learning approach directly from TPS simulations, using a multi-task objective function. Iteratively, this workflow significantly improves shooting efficiency without any prior knowledge of the process. In addition, the optimized CVs can be used with biased enhanced sampling methodologies to accurately reconstruct the free energy profiles. We tested the method on three different systems: a two-dimensional toy model, conformational transitions of alanine dipeptide, and hydrolysis of acetyl chloride in bulk water. In the latter, we integrated our workflow with an active learning scheme to learn a reactive machine learning-based potential, which allowed us to study the mechanism and free energy profile with an ab initio-like accuracy. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2404_02597 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Combining transition path sampling with data-driven collective variables through a reactivity-biased shooting algorithm Zhang, Jintu Zhang, Odin Bonati, Luigi Hou, TingJun Computational Physics Rare event sampling is a central problem in modern computational chemistry research. Among the existing methods, transition path sampling (TPS) can generate unbiased representations of reaction processes. However, its efficiency depends on the ability to generate reactive trial paths, which in turn depends on the quality of the shooting algorithm used. We propose a new algorithm based on the shooting success rate, i.e. reactivity, measured as a function of a reduced set of collective variables (CVs). These variables are extracted with a machine learning approach directly from TPS simulations, using a multi-task objective function. Iteratively, this workflow significantly improves shooting efficiency without any prior knowledge of the process. In addition, the optimized CVs can be used with biased enhanced sampling methodologies to accurately reconstruct the free energy profiles. We tested the method on three different systems: a two-dimensional toy model, conformational transitions of alanine dipeptide, and hydrolysis of acetyl chloride in bulk water. In the latter, we integrated our workflow with an active learning scheme to learn a reactive machine learning-based potential, which allowed us to study the mechanism and free energy profile with an ab initio-like accuracy. |
| title | Combining transition path sampling with data-driven collective variables through a reactivity-biased shooting algorithm |
| topic | Computational Physics |
| url | https://arxiv.org/abs/2404.02597 |