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Weighted Ensemble Simulations With the Drude Polarizable Model.

Marcelo D Polêto1,2, Gabriel Monteiro da Silva3, Brenda M Rubenstein4,5,6

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|November 8, 2025
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Summary
This summary is machine-generated.

This study introduces a new computational method combining enhanced sampling with polarizable force fields for molecular simulations. This approach improves the exploration of complex molecular behaviors and accelerates computational discoveries.

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Area of Science:

  • Computational chemistry and molecular dynamics simulations.
  • Development of advanced simulation methodologies.

Background:

  • Enhanced sampling methods improve exploration of molecular configurations and rare events.
  • Polarizable force fields account for electronic polarization, crucial for accurate simulations of molecular interactions and barriers.
  • Combining these techniques offers synergistic benefits for computational discovery.

Purpose of the Study:

  • To implement and validate a weighted ensemble strategy for the Drude polarizable force field using WESTPA and OpenMM.
  • To demonstrate the utility of this combined approach for conformational sampling and studying functional rotations in biomolecules.

Main Methods:

  • Integration of the WESTPA software package with the OpenMM simulation engine.
  • Application of the weighted ensemble strategy with the Drude polarizable force field.
  • Testing on alanine dipeptide for backbone conformational sampling and Abl1 kinase for sidechain rotations.

Main Results:

  • Successful implementation of the WESTPA-Drude strategy.
  • Demonstrated capability for backbone conformational sampling in a model system.
  • Validated for studying functional sidechain rotations in an enzyme, highlighting the role of polarization.

Conclusions:

  • The WESTPA-Drude implementation enables efficient exploration of configurational space with polarizable force fields.
  • This validated strategy facilitates the study of molecular mechanisms influenced by electronic polarization.
  • The developed tool is expected to be widely adopted by the simulation community for enhanced molecular discovery.