Accelerating Molecular Dynamics through Informed Resetting
Fuente:
arXiv
Salvato in:
| Autori principali: | , , , , , |
|---|---|
| Natura: | Preprint |
| Pubblicazione: |
2024
|
| Soggetti: | |
| Accesso online: | |
| Tags: |
Aggiungi Tag
Nessun Tag, puoi essere il primo ad aggiungerne!!
|
| _version_ | 1866916537099616256 |
|---|---|
| author | Church, Jonathan R. Blumer, Ofir Keidar, Tommer D. Ploutno, Leo Reuveni, Shlomi Hirshberg, Barak |
| author_facet | Church, Jonathan R. Blumer, Ofir Keidar, Tommer D. Ploutno, Leo Reuveni, Shlomi Hirshberg, Barak |
| contents | We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard simulations. We recently showed that stochastic resetting can accelerate molecular simulations that exhibit broad transition time distributions. However, standard stochastic resetting does not exploit any information about the reaction progress. For a model system and chignolin in explicit water, we demonstrate that an informed resetting protocol leads to greater accelerations than standard stochastic resetting in molecular dynamics and Metadynamics simulations. This is achieved by resetting only when a certain condition is met, e.g., when the distance from the target along the reaction coordinate is larger than some threshold. We use these accelerated simulations to infer important kinetic observables such as the unbiased mean first-passage time and direct transit time. For the latter, Metadynamics with informed resetting leads to speedups of 2-3 orders of magnitude over unbiased simulations with relative errors of only ~35-70%. Our work significantly extends the applicability of stochastic resetting for enhanced sampling of molecular simulations. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_10115 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Accelerating Molecular Dynamics through Informed Resetting Church, Jonathan R. Blumer, Ofir Keidar, Tommer D. Ploutno, Leo Reuveni, Shlomi Hirshberg, Barak Chemical Physics Statistical Mechanics Computational Physics We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard simulations. We recently showed that stochastic resetting can accelerate molecular simulations that exhibit broad transition time distributions. However, standard stochastic resetting does not exploit any information about the reaction progress. For a model system and chignolin in explicit water, we demonstrate that an informed resetting protocol leads to greater accelerations than standard stochastic resetting in molecular dynamics and Metadynamics simulations. This is achieved by resetting only when a certain condition is met, e.g., when the distance from the target along the reaction coordinate is larger than some threshold. We use these accelerated simulations to infer important kinetic observables such as the unbiased mean first-passage time and direct transit time. For the latter, Metadynamics with informed resetting leads to speedups of 2-3 orders of magnitude over unbiased simulations with relative errors of only ~35-70%. Our work significantly extends the applicability of stochastic resetting for enhanced sampling of molecular simulations. |
| title | Accelerating Molecular Dynamics through Informed Resetting |
| topic | Chemical Physics Statistical Mechanics Computational Physics |
| url | https://arxiv.org/abs/2409.10115 |