docs: define GROMACS model deviation arguments

[njzjz-bot]

Summary

• replace the empty GROMACS model-deviation variant with a strict schema;
• document per-iteration GROMACS fields, required input files, and trajectory-processing settings;
• include the common selection/cleanup controls used after GROMACS exploration;
• add strict validation coverage for all fields consumed by the current maker and runner.

Tests

• /tmp/dpgen-test-env/bin/python -m unittest tests.test_check_examples -v
• ruff check dpgen/generator/arginfo.py tests/test_check_examples.py
• ruff format --check dpgen/generator/arginfo.py tests/test_check_examples.py

Fixes #771

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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Run ID: 849cf3b4-eb0f-4c82-9b83-d1d82eac68d8

📥 Commits

Reviewing files that changed from the base of the PR and between d5ce577 and e267a05.

📒 Files selected for processing (4)

• dpgen/generator/arginfo.py
• dpgen/generator/run.py
• tests/generator/test_gromacs_engine.py
• tests/test_check_examples.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.84%. Comparing base (d5ce577) to head (e267a05).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1959      +/-   ##
==========================================
+ Coverage   49.80%   49.84%   +0.03%     
==========================================
  Files          83       83              
  Lines       14986    14997      +11     
==========================================
+ Hits         7464     7475      +11     
  Misses       7522     7522              

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[njzjz-bot]

Independent review C

I found no blocking correctness, regression, security, or API issue in this change. CI/check evidence was considered alongside the full patch and relevant surrounding implementation. A formal APPROVE state cannot be submitted because the active njzjz-bot account is the PR author; GitHub self-review rules permit only a COMMENT review here.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent review B

No blocking findings. I reviewed the full diff, relevant surrounding behavior, tests, and current check status. GitHub does not permit njzjz-bot to APPROVE or REQUEST_CHANGES on its own pull request, so this review is recorded as COMMENT only.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent review A

A blocking runtime/schema mismatch is attached inline. GitHub does not permit njzjz-bot to approve or request changes on its own PR, so this COMMENT review records the result as changes needed; no formal review state is claimed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent re-review B

Re-reviewed the current head, including GROMACS argument metadata, input staging semantics, generated MDP handling, and successful CI. I found no blocking issue. No further changes are required from this review.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent re-review C

No changes remain from this independent pass. GitHub does not allow njzjz-bot to formally approve its own PR, so this review is submitted as COMMENT rather than APPROVE.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent re-review A

No remaining correctness issues found at e267a05. I checked the GROMACS schema, staged input-file derivation for default and custom deffnm values, regression coverage, and passing CI. Because this PR is authored by njzjz-bot, GitHub does not permit this account to approve its own PR; this COMMENT means no changes remain from independent re-review A.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh