SAMMD documentation

SAMMD is a configuration-first package for building and exporting self-assembled monolayer chemistry, structure, and parameters. The YAML file describes the surface, SAM chemistry, reactants, solvent, salts, packing, parameterization, and build outputs. OpenMM owns minimization, equilibration, production runs, trajectories, and reporters after those files exist.

If you are new to Python or molecular dynamics, start with installation and pixi basics, then continue to the beginner build workflow. The first command-line build writes sam_grafting_density.cif as a visual smoke test for the slab and SAM grafting density before you need to write a Python script.

The current teaching workflow starts with validation and deterministic build planning, then progresses toward OpenFF/OpenMM-backed system construction and student-written OpenMM simulation scripts.

Tutorials

• Installation and pixi basics
  • 1. Install pixi
  • 2. Clone SAMMD
  • 3. Use the default environment
  • 4. Run one command without entering a shell
  • 5. Switch environments
  • 6. Choose a CUDA environment
  • 7. Use pixi environments as VSCode notebook kernels
  • 8. Next step
• Recommended build-to-OpenMM workflow
  • 1. Create config
  • 2. Validate config
  • 3. Build the starting model
  • 4. Inspect outputs
  • 5. Interchange output files
  • 6. Use these files with OpenMM
  • 7. Other engines
  • Notebook version
• YAML configuration tutorial
  • Minimal starting point
  • Important sections
  • Resolved defaults to notice
  • Limitations in this version
  • Beginner glossary
• OpenMM simulation from SAMMD files
  • Before starting
  • Full copy/paste script
  • Why the step helper functions matter
  • Initial energy check
  • NVT first
  • Optional NPT note
  • About Interchange Reload
  • View the DCD in PyMOL

Reference

• API reference
  • Core workflow
  • Configuration model
  • Orientation analysis helper
• First-release build contract
  • CLI contract
  • Python API contract
  • Validation gates
  • Artifact contract
  • Current limitation

Explanation

• Project scope
• Scientific assumptions
  • Surface and SAM placement
  • Box planning
  • Force-field assumptions
  • Simulation boundary

Contributor guide

• Contributor and developer guide
  • Current package map
  • Development expectations