HeshamFS/md-analysis-planner
skills/simulation-workflow/md-analysis-planner/SKILL.md
Plan molecular dynamics post-processing for materials simulations, including RDF, MSD and diffusion, VACF/VDOS, coordination numbers, bond-angle distributions, stress-strain curves, equilibration detection, PBC unwrapping, and trajectory format choices. Use before writing MD analysis scripts or trusting trajectory-derived results.
$ install --global
skillsauthnpx skillsauth add HeshamFS/materials-simulation-skills md-analysis-plannerInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Last scanned: May 19, 2026, 5:31 AM127.0s5 files scanned
SKILL.md
- name:
- md-analysis-planner
- description:
- >
- allowed-tools:
- Read, Bash, Write, Grep, Glob
- author:
- HeshamFS
- version:
- 1.0.0
- security_tier:
- high
- security_reviewed:
- true
- eval_cases:
- 3
- last_reviewed:
- 2026-05-18
MD Analysis Planner
Goal
Choose the right MD trajectory analyses and prerequisites before writing post-processing code.
Requirements
- Python 3.10+
- No external dependencies
- Works on Linux, macOS, and Windows
Inputs to Gather
| Input | Description | Example |
|-------|-------------|---------|
| System | Material or molecular system | oxide glass, liquid water |
| Goals | Analysis goals | rdf,diffusion,coordination |
| Trajectory format | Dump, DCD, XYZ, H5MD, etc. | LAMMPS dump |
| Velocities | Whether velocities are stored | true |
| Stress | Whether stress/virial is stored | true |
| Unwrap needed | Whether atoms cross PBC | true |
| Timestep | fs per saved frame | 10 |
Decision Guidance
- Use RDF and coordination for local structure.
- Use MSD for diffusion, but unwrap trajectories and verify diffusive regime.
- Use VACF/VDOS only when velocities or reliable finite-difference velocities exist.
- Use stress-strain only if stress/virial and deformation history are available.
- Always perform equilibration checks before fitting transport or thermodynamic properties.
Script Outputs
scripts/md_analysis_planner.py emits:
analysis_planrequired_dataequilibration_checkspbc_handlingwarnings
Workflow
python3 skills/simulation-workflow/md-analysis-planner/scripts/md_analysis_planner.py \
--system "oxide glass" \
--goals rdf,coordination,bond-angle \
--trajectory-format dump \
--unwrap-needed \
--timestep-fs 10 \
--json
Error Handling
If velocities, stress, or timestep information is missing, downgrade dependent analyses and report warnings.
Limitations
This skill plans analysis and prerequisites; it does not parse large trajectories directly.
Security
- Inputs are scalar CLI values and booleans only.
- The script does not read trajectory files or execute external analysis programs.
- The skill uses
Bashonly to run the bundled script.
References
- See
references/md_analysis_checks.mdfor analysis prerequisites and failure modes.
Version History
- 1.0.0: Initial MD analysis planning skill.
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