Short-Time Infrequent Metadynamics for Improved Kinetics Inference
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arXiv
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| Auteurs principaux: | , , |
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| Format: | Preprint |
| Publié: |
2024
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| _version_ | 1866929739328913408 |
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| author | Blumer, Ofir Reuveni, Shlomi Hirshberg, Barak |
| author_facet | Blumer, Ofir Reuveni, Shlomi Hirshberg, Barak |
| contents | Infrequent Metadynamics is a popular method to obtain the rates of long timescale processes from accelerated simulations. The inference procedure is based on rescaling the first-passage times of Metadynamics trajectories using a bias-dependent acceleration factor. While useful in many cases, it is limited to Poisson kinetics, and a reliable estimation of the unbiased rate requires slow bias deposition and prior knowledge of efficient collective variables. Here, we propose an improved inference scheme, which is based on two key observations: 1) The time-independent rate of Poisson processes can be estimated using short trajectories only. 2) Short trajectories experience minimal bias, and their rescaled first-passage times follow the unbiased distribution even for relatively high deposition rates and suboptimal collective variables. Therefore, by limiting the inference procedure to short timescales, we obtain an improved tradeoff between speedup and accuracy at no additional computational cost, especially when employing suboptimal collective variables. We demonstrate the improved inference scheme for a model system and two molecular systems. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_14237 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Short-Time Infrequent Metadynamics for Improved Kinetics Inference Blumer, Ofir Reuveni, Shlomi Hirshberg, Barak Chemical Physics Infrequent Metadynamics is a popular method to obtain the rates of long timescale processes from accelerated simulations. The inference procedure is based on rescaling the first-passage times of Metadynamics trajectories using a bias-dependent acceleration factor. While useful in many cases, it is limited to Poisson kinetics, and a reliable estimation of the unbiased rate requires slow bias deposition and prior knowledge of efficient collective variables. Here, we propose an improved inference scheme, which is based on two key observations: 1) The time-independent rate of Poisson processes can be estimated using short trajectories only. 2) Short trajectories experience minimal bias, and their rescaled first-passage times follow the unbiased distribution even for relatively high deposition rates and suboptimal collective variables. Therefore, by limiting the inference procedure to short timescales, we obtain an improved tradeoff between speedup and accuracy at no additional computational cost, especially when employing suboptimal collective variables. We demonstrate the improved inference scheme for a model system and two molecular systems. |
| title | Short-Time Infrequent Metadynamics for Improved Kinetics Inference |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2401.14237 |