GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation
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arXiv
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| Autori principali: | , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866913298184667136 |
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| author | Ock, Janghoon Mollaei, Parisa Farimani, Amir Barati |
| author_facet | Ock, Janghoon Mollaei, Parisa Farimani, Amir Barati |
| contents | The exploration of molecular systems' potential energy surface is important for comprehending their complex behaviors, particularly through identifying various metastable states. However, the transition between these states is often hindered by substantial energy barriers, demanding prolonged molecular simulations that consume considerable computational efforts. Our study introduces the GradNav algorithm, which enhances the exploration of the energy surface, accelerating the reconstruction of the potential energy surface (PES). This algorithm employs a strategy of initiating short simulation runs from updated starting points, derived from prior observations, to effectively navigate across potential barriers and explore new regions. To evaluate GradNav's performance, we introduce two metrics: the deepest well escape frame (DWEF) and the search success initialization ratio (SSIR). Through applications on Langevin dynamics within Mueller-type potential energy surfaces and molecular dynamics simulations of the Fs-Peptide protein, these metrics demonstrate GradNav's enhanced ability to escape deep energy wells, as shown by reduced DWEF values, and its reduced reliance on initial conditions, highlighted by increased SSIR values. Consequently, this improved exploration capability enables more precise energy estimations from simulation trajectories. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_10358 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation Ock, Janghoon Mollaei, Parisa Farimani, Amir Barati Chemical Physics Computational Engineering, Finance, and Science The exploration of molecular systems' potential energy surface is important for comprehending their complex behaviors, particularly through identifying various metastable states. However, the transition between these states is often hindered by substantial energy barriers, demanding prolonged molecular simulations that consume considerable computational efforts. Our study introduces the GradNav algorithm, which enhances the exploration of the energy surface, accelerating the reconstruction of the potential energy surface (PES). This algorithm employs a strategy of initiating short simulation runs from updated starting points, derived from prior observations, to effectively navigate across potential barriers and explore new regions. To evaluate GradNav's performance, we introduce two metrics: the deepest well escape frame (DWEF) and the search success initialization ratio (SSIR). Through applications on Langevin dynamics within Mueller-type potential energy surfaces and molecular dynamics simulations of the Fs-Peptide protein, these metrics demonstrate GradNav's enhanced ability to escape deep energy wells, as shown by reduced DWEF values, and its reduced reliance on initial conditions, highlighted by increased SSIR values. Consequently, this improved exploration capability enables more precise energy estimations from simulation trajectories. |
| title | GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation |
| topic | Chemical Physics Computational Engineering, Finance, and Science |
| url | https://arxiv.org/abs/2403.10358 |