Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model

Area of Science:

• Computational chemistry
• Biomolecular simulations
• Molecular dynamics

Background:

• Molecular dynamics (MD) simulations with explicit electronic polarization are increasingly used.
• Advances in force field refinement, software optimization, and GPU hardware accelerate these simulations.
• Polarizable MD is crucial for biomolecular systems with complex or unique microenvironments.

Purpose of the Study:

• To provide practical protocols for preparing and analyzing polarizable MD simulations.
• To address the growing need for tutorial material on polarizable MD simulations.
• To demonstrate the application of these methods to protein and peptide systems.

Main Methods:

• Utilized CHARMM for system preparation of proteins in aqueous solvent and transmembrane peptides in lipid bilayers.
• Employed OpenMM for performing the polarizable MD simulations.
• Analyzed dipole moment properties using CHARMM for insights into molecular behavior.

Main Results:

• Successfully prepared and simulated both a globular protein and a model peptide using polarizable force fields.
• Demonstrated protocols for handling heterogeneous and unique microenvironments in biomolecular simulations.
• Provided example input files and detailed steps for reproducibility.

Conclusions:

• Polarizable MD simulations are becoming essential for accurate biomolecular modeling.
• Standardized protocols are vital for the wider adoption and application of polarizable MD.
• This work facilitates the use of polarizable MD for studying complex biological systems.