| name | md-equilibration |
| description | Standalone minimization plus equilibration of a prepared MD system using MDClaw CLI tools, including low-temperature NVT warmup, NVT heating, and optional NPT density. Creates min and eq DAG nodes and writes restart artifacts for production handoff. |
MD Equilibration
You are a computational biophysics expert running MD equilibration 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
Extract parameters from the user's request and present a summary.
If the user specifies a duration in ns/ps/time units, do not convert it to
steps yourself. Use nvt_time_ns / npt_time_ns in node conditions and
--nvt-time-ns / --npt-time-ns when invoking run_equilibration. The tool
will convert durations to steps using the actual timestep_fs.
| Parameter | Value |
|---|
| Target | (job directory) |
| Execution mode | read progress.json.params.execution_mode |
| Temperature | 300 K (default) |
| Pressure | 1.0 bar (default, explicit) / 0 (implicit) |
| Other | (non-default parameters: seed, label, etc.) |
Prerequisites
Follow skills/common/run-loop.md (inspect -> create -> explain -> run). Start
with inspect_job to confirm a completed topo node, then create or reuse the
min/eq node for this stage. The tools auto-resolve system_xml_file,
topology_pdb_file, and state_xml_file from the topo ancestor; eq also
auto-resolves the parent min node's state. If topology metadata contains
ligand charge or clash diagnostics, record them for reporting, but do not choose
a different equilibration protocol.
Workflow
This skill operates on one job_dir. Reuse the same topo node and branch into
multiple eq nodes when you need replicates or different conditions. If
progress.json.params.execution_mode is unset, infer it from the request and
persist it with mdclaw update_workflow_state --params '{"execution_mode":"autonomous"}'.
- Create the
min and eq nodes (see Node Setup below).
- Read and follow the regime page, which owns the platform preflight and the
run_minimization / run_equilibration commands:
- Explicit water ->
skills/md-equilibration/explicit-water.md
- Implicit solvent ->
skills/md-equilibration/implicit-water.md
- Hand off (see Handoff below).
For finer control than one min + eq pair (e.g. NPT compress -> NVT
thermalize -> NPT relax), see skills/md-equilibration/multi-stage-eq.md.
Node Setup
Create nodes first; the regime page runs the tools with --job-dir /
--node-id. --conditions is one quoted JSON string.
mdclaw create_node --job-dir <job_dir> --node-type min \
--label "minimized" \
--conditions '{"max_iterations": 5000,
"restraint_atoms": "solute_heavy",
"restraint_force_constant": 100.0}'
mdclaw create_node --job-dir <job_dir> --node-type eq \
--label "300K" \
--conditions '{"temperature_kelvin": 300, "pressure_bar": 1.0,
"nvt_time_ns": 1.0, "npt_time_ns": 1.0}'
For replicates or alternate conditions, branch a new eq node from the same
min node with --parent-node-ids <min_node_id> and a distinct --label (and
random_seed in --conditions when needed).
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
- Verify the
eq node is completed in progress.json.
- Perform Visual QA per
skills/common/visual-qa.md (render preview, inspect,
register_visual_review). If severity is high, ask the user before
production.
- Follow the stopping rule in
skills/common/run-loop.md. If the current
request continues through production or beyond, invoke
skills/md-production/SKILL.md on this job_dir. Otherwise tell the user:
Equilibration complete. Next:
Continue with skills/md-production/SKILL.md on this job_dir.
Shortcut, if available: /md-production <job_dir>
