force-fields

Force Fields — Molecular Mechanics for MD Simulations

Classical force fields define the potential energy of a molecular system as a sum of bonded and non-bonded terms. The parameters (k, r0, θ0, ε, σ, q) define how molecules move and interact. Python-first stack: OpenMM (engine) + OpenFF toolkit (SMIRNOFF small molecule parameterization).

When to Use This Skill

• Setting up MD simulations with AMBER, CHARMM, or OpenFF force fields
• Parameterizing drug-like small molecules (GAFF2, SMIRNOFF Sage)
• Running energy minimization and MD with OpenMM
• Assigning partial charges (AM1-BCC, RESP)
• Understanding energy terms: bonds, angles, torsions, vdW, electrostatics
• Choosing water model (TIP3P, OPC, TIP4P-Ew)
• Analyzing energy decomposition by force group

Quick Start

# Protein-ligand simulation with OpenMM + OpenFF (SMIRNOFF Sage)
from openff.toolkit import Molecule, ForceField
from openff.toolkit.utils.exceptions import ParameterLookupError
from openmmforcefields.generators import SystemGenerator
import openmm.app as app
import openmm as mm
import openmm.unit as unit

# 1. Load protein topology
pdb = app.PDBFile('protein.pdb')

# 2. Parameterize ligand with OpenFF Sage
ligand = Molecule.from_smiles('c1ccc(cc1)CN')
ligand.generate_conformers(n_conformers=1)

# 3. Build system
system_generator = SystemGenerator(
    forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml'],
    small_molecule_forcefield='openff-2.2.0',
    molecules=[ligand],
    forcefield_kwargs={'nonbondedMethod': app.PME, 'constraints': app.HBonds},
)
system = system_generator.create_system(pdb.topology, molecules=[ligand])

# 4. Run with Langevin integrator
integrator = mm.LangevinMiddleIntegrator(
    300 * unit.kelvin, 1.0 / unit.picosecond, 2.0 * unit.femtoseconds
)
simulation = app.Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy(maxIterations=500)
simulation.reporters.append(app.DCDReporter('traj.dcd', 1000))
simulation.step(50000)  # 100 ps