ArticleJournal of chemical theory and computation2024
Short-Time Infrequent Metadynamics for Improved Kinetics Inference.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Stepping Up Enhanced Rate Calculations with EATR-Flooding.Journal of chemical theory and computation · 2026Article
- Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers.Journal of chemical theory and computation · 2026Article
- Adaptive resetting for informed search strategies and the design of non-equilibrium steady-states.Nature communications · 2025Article
- Residence time in drug discovery: current insights and future perspectives.Pharmacological reports : PR · 2025Review
- Accelerating Molecular Dynamics through Informed Resetting.Journal of chemical theory and computation · 2025Article
- Calculating Protein-Ligand Residence Times through State Predictive Information Bottleneck Based Enhanced Sampling.Journal of chemical theory and computation · 2024Article
- Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach.Journal of chemical theory and computation · 2024Article
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Authors and funding
3 authors.
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Abstract
Infrequent Metadynamics is a popular method to obtain the rates of long time-scale processes from accelerated simulations. The inference procedure is based on rescaling the first-passage times of the 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 basing the inference procedure on short time scales, we obtain an improved trade-off 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.
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Registered trials
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