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name: protocols description: "Choose and configure OpenFE protocol classes, default settings, ProtocolDAG creation, API execution boundaries, OpenMM backend settings, and simulation failure modes." disable-model-invocation: true metadata: disco-role: operating license: MIT

OpenFE Protocols

Use this sub-skill when the task is about selecting an OpenFE protocol class, customizing protocol settings before construction, creating Transformation or ProtocolDAG objects, setting OpenMM backend options, or diagnosing protocol-level simulation failures.

Route Tasks

• Choose among RelativeHybridTopologyProtocol, AbsoluteBindingProtocol, AbsoluteSolvationProtocol, SepTopProtocol, and PlainMDProtocol; see protocol reference.
• Inspect and edit default_settings() safely before protocol construction, including protocol_repeats, lambda/window settings, sampling lengths, output/checkpoint settings, OpenMM platform settings, and optional _adaptive_settings() caveats; see settings and execution.
• Create API-side work with Transformation.create() or protocol.create(...), understand what a ProtocolDAG contains, and know when execute_DAG actually runs expensive simulations; see settings and execution.
• Print protocol default settings without creating systems or running simulations using the defaults inspector.
• Troubleshoot wrong protocol topology, immutable protocol/settings surprises, invalid OpenMM settings, CUDA/PTX/platform issues, optional parameterization packages, analysis warnings, checkpoint/resume boundaries, and wall-time interruptions; see troubleshooting.

Safe Operating Rules

• Treat execute_DAG, openfe quickrun, and any protocol create(...) followed by execution as expensive and potentially file-writing; inspect settings and construct objects only when the user wants API planning.
• Customize the Settings object before constructing the protocol. If a protocol already exists, rebuild a new protocol from a copied or fresh settings object instead of mutating the existing protocol.
• Prefer default_settings() for a known baseline. Use _adaptive_settings() only when the protocol documents it, the required ChemicalSystem and mapping inputs are available, and the user accepts that the method is experimental.
• Use the bundled defaults inspector for safe defaults discovery; it imports protocol classes and serializes settings, but it never builds chemical systems, submits jobs, runs OpenMM, or downloads data.
• Keep protocol guidance separate from execution orchestration: CLI command syntax and scheduler command generation belong in ../cli-workflows/SKILL.md, and post-run estimates or gathered tables belong in ../results-analysis/SKILL.md.

Boundary Handoffs

• Ligand/protein/solvent loading, ChemicalSystem construction, atom mapping, and ligand-network planning belong in ../network-planning/SKILL.md.
• CLI flags, openfe quickrun, resume command syntax, repeat-safe shell/Slurm command generation, and gather command selection belong in ../cli-workflows/SKILL.md.
• Result JSON decoding, ProtocolResult.get_estimate(), uncertainty interpretation, plots, and network result aggregation belong in ../results-analysis/SKILL.md.