Parameterization of General Organic Polymers within the Open Force Field Framework.

Area of Science:

• Computational chemistry
• Materials science
• Biophysics

Background:

• Traditional molecular simulation workflows struggle with polymer and biopolymer parameterization due to insufficient chemical information in standard formats like PDB.
• Large polymer sizes hinder accurate partial charge generation, complicating simulation preparation.

Purpose of the Study:

• To develop a flexible and comprehensive molecular simulation workflow for organic polymers and soft materials.
• To introduce a novel input specification for monomer information to facilitate parameterization and simulation.

Main Methods:

• Utilized direct chemical perception via the Open Force Field toolkit.
• Developed a new monomer input specification using SMIRKS for chemical identification and charge assignment.
• Integrated automatic partial charge generation methods for large systems.
• Parametrized diverse systems including proteins, DNA, homopolymers, and sugars.

Main Results:

• Successfully parametrized various polymeric systems using the Open Force Field toolkit.
• Demonstrated a start-to-finish workflow for simulation and property prediction for poly(ethylene glycol), polyacrylamide, and poly(N-isopropylacrylamide).
• Computed shape properties and radial distribution functions, comparing them to existing simulation data.

Conclusions:

• The proposed workflow and monomer specification effectively parametrize and simulate soft-matter systems.
• This approach significantly expedites computational research in soft-matter simulations.
• Establishes a robust atomic-scale polymer specification compatible with existing notations.