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

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.