EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation
Fuente:
arXiv
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| Autori principali: | , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866915496295661568 |
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| author | Cao, Hai-Ming Li, Bin |
| author_facet | Cao, Hai-Ming Li, Bin |
| contents | The molecular dynamics (MD) simulation technique has been widely used in complex systems, but the accessible time scale is limited due to the requirement of small integration timesteps. Here, we propose a novel method, named Exploratory dynamics Sampling with recursion (EdSr), inspired by ordinary differential equation and Taylor expansion formula, which enables flexible adjustment of timestep in MD simulations. By setting up four groups of experiments including simple functions, ideal physical models, all-atom simulations and coarse-grained simulations, we demonstrate that EdSr can dynamically and flexibly adjust the simulation timestep according to the requirements during simulation period, and operate with larger timesteps than the widely used velocity-Verlet integrator. Although the method can not perform perfectly at flexible timestep across all simulation systems, we believe that it provides a promising direction for future studies. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2412_20978 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation Cao, Hai-Ming Li, Bin Computational Physics The molecular dynamics (MD) simulation technique has been widely used in complex systems, but the accessible time scale is limited due to the requirement of small integration timesteps. Here, we propose a novel method, named Exploratory dynamics Sampling with recursion (EdSr), inspired by ordinary differential equation and Taylor expansion formula, which enables flexible adjustment of timestep in MD simulations. By setting up four groups of experiments including simple functions, ideal physical models, all-atom simulations and coarse-grained simulations, we demonstrate that EdSr can dynamically and flexibly adjust the simulation timestep according to the requirements during simulation period, and operate with larger timesteps than the widely used velocity-Verlet integrator. Although the method can not perform perfectly at flexible timestep across all simulation systems, we believe that it provides a promising direction for future studies. |
| title | EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation |
| topic | Computational Physics |
| url | https://arxiv.org/abs/2412.20978 |