ArticleCommunications chemistry2024
Convergence and equilibrium in molecular dynamics simulations.
Article in Communications chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Structural insights into PFAS-β-lactoglobulin binding mechanism mediating PFAS toxicity.bioRxiv : the preprint server for biology · 2026Article
- Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time.ArXiv · 2026Article
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- Multi-omics integration reveals CYP2B6 as a central node in the molecular landscape of non-small cell lung cancer.Medical oncology (Northwood, London, England) · 2025Article
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- Probing the microRNA landscape in cadmium chloride induced renal toxicity through an in silico approach.Scientific reports · 2025Article
- UFMylation: A supervisor of the HIF1α pathway and a potential therapeutic target for anti-PD-1 combination therapy in hypoxic tumors.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Larvicidal potential of Knoevenagel adducts againstFuture medicinal chemistry · 2025Article
- Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.RSC chemical biology · 2025Review
- A Review on Perception of Binding Kinetics in Affinity Biosensors: Challenges and Opportunities.ACS omega · 2025Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics is a powerful tool that has been long used for the simulation of biomolecules. It complements experiments, by providing detailed information about individual atomic motions. But there is an essential and often overlooked assumption that, left unchecked, could invalidate any results from it: is the simulated trajectory long enough, so that the system has reached thermodynamic equilibrium, and the measured properties are converged? Previous studies showed mixed results in relation to this assumption. This has profound implications, as the resulting simulated trajectories may not be reliable in predicting equilibrium properties. Yet, this is precisely what most molecular dynamics studies do. So the question arises: are these studies even valid?Here, we present a thorough analysis of up to a hundred microseconds long trajectories, of several system with varying size, to probe the convergence of different structural, dynamical and cumulative properties, and elaborate on the relevance of the concept of equilibrium, and its physical and biological meaning. The results show that properties with the most biological interest tend to converge in multi-microsecond trajectories, although other properties-like transition rates to low probability conformations-may require more time.
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Registered trials
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