openmm-molecular-dynamics

name	openmm-molecular-dynamics
description	Build, equilibrate, run, checkpoint, and analyze reproducible molecular dynamics with OpenMM. Use for proteins, nucleic acids, solvated complexes, or parameterized protein-ligand systems when local CPU/GPU simulation is requested.
license	MIT

OpenMM Molecular Dynamics

Gate

Follow $cx-compute-environment. Ask once before installing pinned OpenMM and force-field packages and before GPU/long compute. State estimated system size, hardware, wall time, and output size.

Workflow

1. Audit structures with $cx-molecular-input-preparation; parameterize ligands with $cx-openff-parameterization or another explicitly validated method.
2. Record force fields, water model, ions/concentration, periodic box, constraints, nonbonded method/cutoff, timestep, integrator, thermostat/barostat, platform, precision, random seeds, and OpenMM/plugin versions.
3. Build and serialize the topology/system. Minimize, then equilibrate through explicit restrained stages; inspect energy, temperature, pressure, density, clashes, and constraint failures before production.
4. Run production in checkpointed chunks. Keep state/checkpoint, trajectory, logs, serialized system, and exact driver/config under artifacts/<run-id>/openmm/.
5. Analyze prespecified observables with $cx-mdanalysis-trajectory-analysis. Estimate equilibration and autocorrelation; report uncertainty from effective samples or independent replicas.

Boundaries

• One short trajectory is not an equilibrium ensemble or proof of stability.
• Do not compare force-field potential energies to experimental free energies.
• Checkpoint resume must preserve system, integrator state, and random-seed provenance; never present concatenated incompatible stages as one trajectory.