Welcome to VerMoUTH’s documentation!

Contents:

• General Overview
  • Installation instructions
  • Quickstart
  • General layout
  • Citing
  • References
• Martinize 2 workflow
  • Pipeline
  • 1) Read input files
  • 2) Repair the input graph
  • 3) Resolution transformation
  • 4) Apply Links
  • 5) Post processing
  • 6) Write output
• Technical background
  • Processor
  • Data
  • Graph algorithms
• File formats
  • Data structures and file formats
  • Force field file (.ff)
  • Mapping files (.map & .mapping)
• Tutorials
  • Basic usage
  • Elastic Networks
  • Gō models
  • Water biasing
  • Mutations and modifications
  • Adding new residues and links
  • Adding new modifications
• vermouth
  • vermouth package
• Gromacs variables
  • FLEXIBLE
  • POSRES
  • POSRES_FC

Indices and tables

• Index

• Module Index

• Search Page