Functionality

To support diverse use cases, WebDFF functionality is limited to a subset of the DFF Standard edition, which includes:

• Input model file format: MOL2
• Force field types: AMBER and TEAM
• Simulation engines: LAMMPS and GROMACS
• Target systems: soft materials including molecular or ionic liquids, polymers, and biomolecules. Pure and mixed systems are supported.

What WebDFF Does

• Import the model and convert it to DFF data structure
• Rebuild bond orders to ensure consistency, especially for compounds with alternative bonding representations
• Assign formal charges by assuming the most common forms (e.g., isolated metals are treated as ions)
• Assign atom types and search TEAMFF for the best matching parameters. Multiple force field tables may be used. However, intramolecular parameters for molecules are taken completely from a single force field table to maximize transferability; intermolecular parameters are calculated using combination rules. Transferred and estimated parameters are allowed to achieve maximum coverage.
• Integrate parameters from different tables into a single unified force field and export them to topology and structure files, along with an input script for the selected simulation engine.