MartiniSurf Documentation

MartiniSurf is a toolkit to build surface-immobilized biomolecular systems in Martini simulations

Contents

• Overview
  • Main capabilities
  • Output structure
• Installation
  • Local installation
  • External tools required
  • Quick checks
  • Build docs locally
• Recommended Examples
  • Protein + Not explicit Linker + solvate + ionize
  • DNA + linker + solvate + ionize + frozen water
  • Pre-CG protein+cofactor + substrate + solvate + ionize
  • Protein build-only examples
  • DNA build-only examples
  • Surface-focused examples
  • Adsorption mode note
• CLI Overview
  • Compact package help
  • Full package help
  • Main pipeline help
  • Adsorption mode (--ads-mode)
  • Module helps
• MartiniSurf Quick Guide for New Users
  • 1) 30-second rules
  • 2) Minimum installation
  • 3) Pick your workflow
  • 4) Copy-and-run commands
  • 5) Flags you will use most often
  • 6) Full flag reference (martinisurf main pipeline)
  • 7) Advanced flags (internal modules)
  • 8) Output structure to check
  • 9) Common errors and direct fixes
  • 10) Practical checklist before long runs
  • 11) Short software evaluation
  • 12) Colab behavior notes

Quick links

• Source repository: README.md (root)

• Full user guide: MartiniSurf Quick Guide for New Users

• Recommended complete examples: Recommended Examples