prepmd documentation

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Contents:

• Installation
• Quickstart
• prepmd
  • prepmd package
• Preparing structure files for simulation with prepmd
  • prepmd workflow
  • prepmd command-line reference
  • Worked examples
• Running MD simulations with runmd
• runmd command-line reference
  • Output files
  • Explicit solvent
  • Temperature and pressure
  • Change force field
  • Equilibrate only side chains:
  • Add ligands
  • Create a morph trajectory
  • Numerical integrators
  • Other settings
• What next?
• Python API
• Developer notes
  • Dependencies
  • Manual install
  • Code structure
  • Style