How do I install the Md Analysis Planner skill?

Run npx skillmds@latest add zuoguyoupan2023/md-analysis-planner in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Md Analysis Planner safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: executes scripts. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Md Analysis Planner?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Md Analysis Planner free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Md Analysis Planner?

zuoguyoupan2023 (@zuoguyoupan2023) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Md Analysis Planner by zuoguyoupan2023

Name: Md Analysis Planner
Rating: 4.666666666666667 (3 reviews)
Author: zuoguyoupan2023

Md Analysis Planner

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.

File contents

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_plan
required_data
equilibration_checks
pbc_handling
warnings

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 Bash only to run the bundled script.

References

See references/md_analysis_checks.md for analysis prerequisites and failure modes.

Version History

1.0.0: Initial MD analysis planning skill.

---name: md-analysis-plannerdescription: 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.---# MD Analysis Planner## GoalChoose 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_plan`- `required_data`- `equilibration_checks`- `pbc_handling`- `warnings`## Workflow```bashpython3 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 HandlingIf velocities, stress, or timestep information is missing, downgrade dependent analyses and report warnings.## LimitationsThis 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 `Bash` only to run the bundled script.## References- See `references/md_analysis_checks.md` for analysis prerequisites and failure modes.## Version History- 1.0.0: Initial MD analysis planning skill.

Frequently asked questions