molecular-dynamics

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

Quality

73%

Does it follow best practices?

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Securityby

Passed

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tessl review fix ./skills/molecular-dynamics/SKILL.md

Quality

Content

65%

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A highly actionable skill body with clear end-to-end simulation and analysis workflows, weakened by verbosity and an orphaned reference file that is never linked from the main content.

Suggestions

Link references/mdanalysis_analysis.md from the body (e.g., a '## Advanced Analysis' section pointing to it) and move the inline contact/PCA/FES detail there to slim the main file.

Add explicit validation gates between stages, e.g. 'Confirm minimized energy is stable before starting NVT' and 'Verify NVT temperature has equilibrated before NPT'.

Trim repeated import blocks and lengthy docstrings, and remove the generic overview sentence defining molecular dynamics.

Dimension	Reasoning	Score
Conciseness	Mostly efficient executable code, but padded with verbose docstrings, repeated `from openmm.app import *` import blocks, and an overview explaining what MD is — concepts Claude already knows; it could be tightened.	2 / 3
Actionability	Provides fully executable, copy-paste-ready code for system prep, minimization, NVT/NPT, and RMSD/RMSF/contact analysis, plus a force-field selection table and parameterization snippet.	3 / 3
Workflow Clarity	Steps are clearly numbered (System Preparation → Minimization → NVT → NPT → Analysis) with energy logging and checkpoints, but there are no explicit 'proceed only when X' validation gates, so checkpoints remain implicit.	2 / 3
Progressive Disclosure	Sections are well-organized and a reference file (references/mdanalysis_analysis.md) exists, but the body never links to it and inlines analysis code that could live in the reference, so the bundle structure is underused and references are not signaled.	2 / 3
	Total	9 / 12 Passed

Description

82%

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A specific, well-targeted description with strong natural trigger terms and a distinct niche. Its main weakness is the absence of an explicit 'Use when...' trigger clause, leaving the activation guidance only implied.

Suggestions

Add an explicit trigger clause such as 'Use when the user wants to run or analyze molecular dynamics simulations, mentions OpenMM/MDAnalysis, or asks about RMSD, RMSF, free energy, or drug binding.'

Reframe 'For structural biology, drug binding, and biophysics' into user-facing 'when to use' phrasing rather than application-domain tags.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions: 'Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces)' — matching the anchor for several specific concrete actions.	3 / 3
Completeness	The 'what' is detailed and explicit, but the 'when' is only an implied domain tag ('For structural biology, drug binding, and biophysics') rather than an explicit 'Use when...' trigger clause, which the guideline caps at 2.	2 / 3
Trigger Term Quality	Covers natural terms an MD user would say — 'molecular dynamics simulations', 'OpenMM', 'MDAnalysis', 'RMSD', 'RMSF', 'free energy surfaces', 'drug binding' — giving good coverage of domain vocabulary.	3 / 3
Distinctiveness Conflict Risk	A clear niche (molecular dynamics with OpenMM/MDAnalysis) with tool-specific triggers unlikely to conflict with other skills.	3 / 3
	Total	11 / 12 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: K-Dense-AI/scientific-agent-skills
Path: skills/molecular-dynamics/SKILL.md
Commit: 757b63b

Reviewed: about 11 hours ago

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