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Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological

Christopher Kang1, Cheng Giuseppe Chen2, Chenyu Tang2

  • 1Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.

Nature Communications
|June 12, 2026
PubMed
Summary

Enhanced-sampling molecular dynamics methods show unreliable performance across different biological simulations. Standard convergence checks are insufficient, necessitating cross-method validation for accurate free-energy profiles.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Molecular Dynamics Simulations

Background:

  • Enhanced-sampling molecular dynamics is crucial for studying complex biomolecular processes.
  • Its reliability in realistic biological systems is not well understood.

Purpose of the Study:

  • To compare the performance of four enhanced-sampling methods: replica-exchange umbrella sampling (REUS), well-tempered metadynamics (WT-MtD), well-tempered metadynamics-extended adaptive-biasing force (WTM-eABF), and on-the-fly probability enhanced sampling (OPES).
  • To evaluate these methods across five diverse, experimentally relevant biological processes: ligand binding, conformational change, kinase activation, membrane permeation, and ion conduction.

Main Methods:

  • Comparative analysis of REUS, WT-MtD, WTM-eABF, and OPES.
  • Application to five distinct biomolecular systems with experimental grounding.

Main Results:

  • Method performance is context-dependent and does not generalize across different biological scenarios.
  • Failure modes specific to realistic biological landscapes were observed, which are missed in simpler models.
  • Standard self-consistency metrics for assessing simulation convergence are inadequate, as they can indicate convergence for quantitatively incorrect results.

Conclusions:

  • Cross-method validation against independent references is essential for reliable free-energy calculations.
  • Method selection for enhanced-sampling molecular dynamics should be based on the specific biological context.
  • Establishing cross-method validation as a community standard is recommended for improving simulation accuracy.