---

name: force-fields-modeling description: "Choose and troubleshoot OpenMM force fields, model-building workflows, parameterized input formats, and ForceField XML authoring. Use when working with ForceField.createSystem, Modeller, bundled force-field XML files, residue template failures, solvation/hydrogenation/membranes, AMBER/CHARMM/GROMACS/Tinker inputs, or ffxml validation." disable-model-invocation: true metadata: disco-role: operating license: MIT, GPL, LGPL

Force Fields and Modeling

Use this sub-skill when a task is about preparing a molecular model or parameterizing it before a simulation in OpenMM.

Route Here For

• Selecting bundled OpenMM ForceField XML files, compatible water/ion files, implicit solvent files, or polarizable force fields.
• Calling ForceField.createSystem() with correct nonbondedMethod, cutoff, constraints, rigidWater, hydrogenMass, residue template, and external-bond options.
• Editing structures with Modeller: add missing hydrogens, solvent, ions, membranes, extra particles, or remove incompatible water.
• Diagnosing No template found for residue and related residue-template, terminal variant, water-model, bond, or extra-particle mismatches.
• Loading parameterized inputs from AMBER, CHARMM, GROMACS, or Tinker instead of using ForceField XML directly.
• Authoring or validating practical OpenMM force-field XML (ffxml) files and residue template generators.

Start With These References

• references/forcefield-api-and-data.md for ForceField, bundled XML families, createSystem() options, and AMBER/CHARMM/GROMACS/Tinker input routes.
• references/model-building-recipes.md for Modeller workflows: hydrogens, solvent, ions, water conversion, membranes, and extra particles.
• references/forcefield-xml-authoring.md for ffxml structure, residue templates, patches, standard force tags, custom force wiring, and template generators.
• references/troubleshooting.md for template mismatch diagnosis, water/ion compatibility, periodic-box and include-path problems.

Practical Workflow

1. Identify whether the inputs are coordinates plus topology needing a ForceField, or already-parameterized files such as AMBER prmtop, CHARMM psf, GROMACS top, or Tinker xyz/key/prm.
2. Choose force-field XML files as a compatible set: main biopolymer file plus the matching water/ion or implicit-solvent file when needed.
3. Use Modeller before createSystem() when the topology lacks hydrogens, solvent, membranes, or force-field-required extra particles.
4. Run forcefield.getUnmatchedResidues(topology) or forcefield.getMatchingTemplates(topology) before debugging a full simulation when template matching is uncertain.
5. Build the System with createSystem() using nonbonded settings that match the topology: periodic boxes generally pair with PME/cutoffs; implicit solvent supports only non-periodic or limited cutoff choices.
6. Keep production dynamics, integrator choice, reporter setup, and platform precision decisions in sibling sub-skills unless they directly affect model parameterization.

Bundled Script

Use scripts/forcefield_modeling_check.py as a lightweight smoke check for an OpenMM installation and a minimal force-field/model-building path. It builds a tiny in-memory water topology, verifies template matching, creates a System, and prints a JSON summary without requiring source checkout files.

python scripts/forcefield_modeling_check.py

Boundaries

• For running or restarting complete simulations, use simulation-workflows.
• For custom mathematical force expressions or custom integrator algorithms beyond ffxml wiring, use custom-forces-integrators.
• For CUDA/OpenCL/HIP/CPU platform selection, precision, and performance tuning, use platforms-performance.
• For modifying OpenMM internals, plugins, C++ extension development, or tests, use development-extensions.