md-production

name	md-production
description	Production molecular dynamics simulation using MDClaw CLI tools and OpenMM. Runs MD from an equilibrated state, with HMR, restart, and HPC submission support.

MD Production

You are a computational biophysics expert running production MD simulations using MDClaw CLI tools.

Read skills/common/preamble.md, skills/common/tool-output.md, skills/common/run-loop.md, skills/common/solvent-regimes.md, and skills/common/guardrail-codes.md before acting. run-loop.md is the single canonical loop and node-CLI-invariant reference.

Step 0: Parse and Confirm

Parameter	Value
Target	(job directory)
Execution mode	read progress.json.params.execution_mode
Parent eq node	use a completed eq node from inspect_job, or an explicit branch parent
Simulation time	user-specified; plan-derived for a scientific answer; or 0.1 ns only for an omitted production-only sanity run
Other	(non-default parameters)

Prerequisites

Follow skills/common/run-loop.md. Start with mdclaw inspect_job --job-dir <job_dir> to confirm there is a completed eq node, no conflicting running work, and the intended solvent_regime. For an extension, use --continue-from (below) rather than a default forward edge. Use IDs from inspect_job, explain_node, and create_node, never literal example IDs from documentation. For a candidate prod node, mdclaw explain_node --job-dir <job_dir> --node-id <prod_node_id> reports ready_to_run and validation.blocking_codes. (system_xml_file, topology_pdb_file, state_xml_file, and restart_from are auto-resolved from DAG ancestors by the tool. For convenience, pressure_bar defaults to the eq node's metadata.final_ensemble so the common eq → prod handoff matches by default. You can override --pressure-bar to switch ensembles freely — the saved eq state is reusable across NPT/NVT thanks to the ensemble-agnostic loader. See skills/md-production/restart.md "Switching Ensembles Across Nodes" for details.)

If no completed eq node exists, suggest running skills/md-equilibration/SKILL.md on the same job_dir first (/md-equilibration <job_dir> when slash commands are available).

Default Decision Rule

• If the current request asks for a scientific answer, use its explicit production length or the study plan's budget.derived.target_ns_per_replicate and target_replicates_per_job. If neither exists, return to md-study planning or ask for a length before creating a production node. Never use the 0.1 ns sanity default as evidence for a scientific conclusion.
• If execution_mode=autonomous, the stopping point is production, and the user omitted a length, adopt simulation_time_ns=0.1 as a direct-run sanity check. This is skill policy; the underlying CLI default remains the tool signature.
• If the job belongs to a study with study_plan.json, treat its plan as the scientific intent. The plan may guide production length, replicates, and branch labels, but it is not required for ordinary single-system runs.
• If execution_mode=human_in_the_loop and the user did not specify a production length, ask before choosing a run length.
• If the user explicitly asks for a longer campaign or HPC submission, prefer the user's stated intent. HPC submission still requires explicit current authorization.

Node Setup

mdclaw create_node --job-dir <job_dir> --node-type prod \
  --label "100ns" \
  --conditions '{"simulation_time_ns": 100}'

--conditions is one JSON string argument; quote it as shown.

Branching (multiple prod from same eq):

mdclaw create_node --job-dir <dir> --node-type prod --parent-node-ids <eq_node_id> \
  --label "100ns_seed42" --conditions '{"simulation_time_ns": 100, "random_seed": 42}'

Extension (continue from a completed prod — preferred way to extend):

mdclaw create_node --job-dir <dir> --node-type prod \
  --continue-from <completed_prod_node_id> \
  --label "+50ns" --conditions '{"simulation_time_ns": 50}'

Custom force / CV bias: pass --custom-force-script (an energy(positions, ctx) function, autograd computes the forces via PythonTorchForce) to run_production; the bias signature and artifacts are auto-recorded on the node (do not hand-declare custom_force in --conditions — it is validated by exact match and would fail). See skills/md-production/custom-force.md.

For normal use, --continue-from is the only extension detail the agent needs. If a run is being retried, chained, or debugged, read skills/md-production/restart.md.

Workflow

This skill operates on one job_dir. Branch from the same eq node for replicates or alternate conditions, and use --continue-from when extending an existing production branch.

If mode metadata is missing, infer it from the current request and persist it with mdclaw update_workflow_state --params ... before creating new prod nodes.

1. Based on solvent type:
   • Explicit water -> Read and follow skills/md-production/explicit-water.md
   • Implicit solvent -> Read and follow skills/md-production/implicit-water.md

To apply a biasing potential (positional restraint, distance / domain bias, or a candidate collective variable for CV exploration), read and follow skills/md-production/custom-force.md — you write a single energy(positions, ctx) function and MDClaw computes the forces by autograd, logging bias energy and CV values for analysis.

Error Handling

Follow skills/common/tool-output.md: branch on stable code values, never parse stderr, and do not retry a failed command with identical parameters.

Handoff

1. Verify the prod node is completed.
2. Perform Visual QA per skills/common/visual-qa.md (render preview, inspect, register_visual_review; --style publication for the final structure, --style ligand_site / --style membrane when relevant). If severity is high, ask the user before using the production output downstream.
3. Follow the stopping rule in skills/common/run-loop.md. If the current request requires analysis or a scientific answer, invoke skills/md-analyze/SKILL.md on this job_dir. Otherwise present:

   Production complete. Next:
     Continue with skills/md-analyze/SKILL.md on this job_dir.
     Shortcut, if available: /md-analyze <job_dir>
   
   To branch from same equilibration:
     Run this production skill again on the same job_dir.
     Shortcut, if available: /md-production <job_dir>