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.

Respond in the user's language. Use English for tool parameter values. All MDClaw tools are invoked via Bash with the mdclaw command. Output is JSON on stdout.

Step 0: Parse and Confirm

Parameter	Value
Target	(job directory)
Execution mode	read `progress.json.params.execution_mode`
Parent eq node	(eq_001, etc.)
Simulation time	user-specified, or `0.1 ns` skill-level sanity check when omitted in autonomous mode
Other	(non-default parameters)

Prerequisites

Read progress.json -- find a completed eq node. (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 /md-equilibration <job_dir> first.

Default Decision Rule

If execution_mode=autonomous and the user did not specify a production length, adopt simulation_time_ns=0.1 as the default sanity check run length and proceed without asking. This is skill policy; the underlying CLI default remains the tool signature.
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, HPC submission, or a specific scientific objective, prefer the user's stated intent over the 0.1 ns default.

Node Setup

mdclaw create_node --job-dir <job_dir> --node-type prod \
  --parent-node-ids eq_001 \
  --label "100ns" \
  --conditions '{"simulation_time_ns": 100}'

Branching (multiple prod from same eq):

mdclaw create_node --job-dir <dir> --node-type prod --parent-node-ids eq_001 \
  --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 prod_001 \
  --label "+50ns" --conditions '{"simulation_time_ns": 50}'

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_job_params before creating new prod nodes.

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

Error Handling

Use structured JSON fields from tool output to decide next steps. Never parse stderr or warning strings to make decisions.
Branch on stable code values when present; otherwise report the structured errors / warnings fields.
Retrying the same failed command with identical parameters will produce the same error.

Handoff

Verify prod node status is completed.

Present:

Production complete. Next:
  /md-analyze <job_dir>

To branch from same equilibration:
  /md-production <job_dir>

/md-production does not auto-invoke analysis — /md-analyze is always a user-initiated follow-up step.

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.