prepmd documentation

A utility to automatically prepare structures from the PDB for molecular dynamics simulation and perform minimisations and simple MD simulations. Source: https://github.com/CCPBioSim/prepmd

Contents:

• Installation
• Quickstart
• Preparing structure files for simulation with prepmd
  • prepmd workflow
  • prepmd command-line reference
  • Worked examples
• Running MD simulations with runmd
  • runmd workflow
  • runmd command-line reference
  • Example usage
• What next?
• Python API
• Developer notes
  • Dependencies
  • Manual install
  • Code structure
  • Style
• prepmd
  • prepmd package