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CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.

Abhishek A Kognole1, Jumin Lee2, Sang-Jun Park2

  • 1Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA.

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|December 7, 2021
PubMed
Summary

Drude Prepper simplifies using polarizable force fields (FFs) for molecular simulations. This CHARMM-GUI tool generates necessary files for accurate modeling of electronic structure variations in complex systems.

Keywords:
DNARNAcarbohydratedipole momentmembraneproteinprotein structure file

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Area of Science:

  • Computational chemistry and biophysics
  • Molecular dynamics simulations
  • Force field development

Background:

  • Traditional additive force fields (FFs) do not account for electronic polarizability, limiting realism in simulations.
  • Polarizable FFs offer a more accurate representation of electronic structure changes in condensed phases and macromolecules.
  • The classical Drude oscillator model is a key approach for implementing polarizable FFs.

Purpose of the Study:

  • To develop and validate Drude Prepper, a CHARMM-GUI tool for generating inputs for polarizable force field (pFF) simulations.
  • To streamline the utilization of Drude oscillator-based pFFs in molecular dynamics (MD) simulations.
  • To facilitate the application of pFFs to diverse condensed-phase and macromolecular systems.

Main Methods:

  • Drude Prepper ingests existing molecular structure files (PSF, PDB, NAMD) to identify system components.
  • It constructs Drude FF-based parameter files (PSF) using CHARMM's molecular generation capabilities.
  • Input generation for MD simulation packages including CHARMM, GROMACS, NAMD, and OpenMM.

Main Results:

  • Successful generation of Drude FF-based simulation inputs for various systems (proteins, nucleic acids, lipids, ions).
  • Stable 5-microsecond MD simulations achieved for ubiquitin, validating the generated Drude PSFs.
  • Demonstrated ability of the Drude FF to model electronic structure variations via dipole moment analysis.

Conclusions:

  • Drude Prepper effectively facilitates the use of Drude oscillator-based polarizable force fields in molecular simulations.
  • The tool ensures the integrity of generated parameter files, enabling stable and accurate MD simulations.
  • Drude Prepper is expected to significantly advance the application of pFFs in complex biological and condensed-phase systems.