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Output Structure

OpenBuilder writes all builds into the outputs/ directory.

📁 Project Folder

Each build creates a self-contained project:

outputs/OpenBuilder-YYYY-MM-DD_HH-MM-SS/
├── config.json
├── user_inputs/
├── simulations/
├── toppar/
└── mdp/

📄 config.json

Stores the full configuration used for the build.

  • Enables full reproducibility
  • Can be reused with CLI mode

🧬 user_inputs/

Contains all uploaded input files:

user_inputs/
├── protein.pdb
└── protein.itp

These files are copied automatically and included in the final ZIP.

🔁 simulations/

Contains one folder per replica:

simulations/
├── R0001/
├── R0002/
└── R0003/

Each folder includes:

  • generated system files
  • topology (topol.top)
  • simulation outputs (.gro, etc.)

⚛️ toppar/

Contains force field and topology files:

  • Martini force field files
  • protein topology (protein.itp)

🧪 mdp/

Contains simulation parameter files:

  • energy minimization (em.mdp)
  • equilibration (eq*.mdp)
  • production (md.mdp)

📦 ZIP Archive

A compressed copy of the entire project is automatically created:

downloads/OpenBuilder-YYYY-MM-DD_HH-MM-SS.zip

This archive includes everything needed to reproduce the system.

✅ Summary

Each build is:

  • Fully self-contained
  • Reproducible via config.json
  • Ready for simulation workflows