Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine...

Area of Science:

• Computational Chemistry
• Molecular Dynamics
• Biophysics

Background:

• The POlarizable Simulations with Second order Interaction Model (POSSIM) force field is crucial for simulating molecular systems.
• Previous versions focused on general protein simulations.
• Accurate force fields are essential for predicting molecular behavior.

Purpose of the Study:

• To extend the POSSIM force field with parameters for alanine peptides and protein backbones.
• To refine the fitting protocol for polarizable protein force fields.
• To validate the accuracy of the extended force field against quantum mechanical calculations.

Main Methods:

• Developed new parameters for alanine peptides and protein backbones within the POSSIM framework.
• Implemented a refined fitting protocol using reduced quantum mechanical data for electrostatic parameters.
• Validated the force field by calculating binding energies, geometries, conformational energies, and backbone angles for peptides and an alpha-helix.

Main Results:

• The extended POSSIM force field demonstrated good agreement with high-level quantum mechanical results for binding energies and geometries of alanine dipeptide complexes.
• Calculated conformational energies and backbone angles for alanine di- and tetra-peptides showed adequate agreement with QM data.
• Simulations of an alpha-helix in gas-phase and water confirmed the backbone conformational behavior.

Conclusions:

• The enhanced POSSIM force field provides accurate parameters for alanine peptides and protein backbones.
• The refined fitting protocol and validated parameters advance the development of fast, polarizable force fields for proteins.
• This work supports the use of POSSIM for detailed molecular simulations in computational chemistry and biophysics.