ArticleNature communications2024
Combining stochastic resetting with Metadynamics to speed-up molecular dynamics simulations.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
8 citing papers in PubMed.
- Structure-Based Design and In Silico Evaluation of a Lipophilic Cyclooctanoyl- Derivative as a Renin Inhibitor: Lessons from Withdrawn Aliskiren.International journal of molecular sciences · 2025Article
- Adaptive resetting for informed search strategies and the design of non-equilibrium steady-states.Nature communications · 2025Article
- Ion-Induced Dipole Interactions Matter in Metadynamics Simulation of Transition Metal Ion Transporters.Journal of chemical theory and computation · 2025Article
- Accelerating Molecular Dynamics through Informed Resetting.Journal of chemical theory and computation · 2025Article
- Restart uncertainty relation for monitored quantum dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Computational Fluid-Structure Interaction in Microfluidics.Micromachines · 2024Review
- Short-Time Infrequent Metadynamics for Improved Kinetics Inference.Journal of chemical theory and computation · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective variables are usually not known a priori and finding them can be very challenging. We recently presented a collective variables-free approach to enhanced sampling using stochastic resetting. Here, we combine the two methods, showing that it can lead to greater acceleration than either of them separately. We also demonstrate that resetting Metadynamics simulations performed with suboptimal collective variables can lead to speedups comparable with those obtained with optimal collective variables. Therefore, applying stochastic resetting can be an alternative to the challenging task of improving suboptimal collective variables, at almost no additional computational cost. Finally, we propose a method to extract unbiased mean first-passage times from Metadynamics simulations with resetting, resulting in an improved tradeoff between speedup and accuracy. This work enables combining stochastic resetting with other enhanced sampling methods to accelerate a broad range of molecular simulations.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.