Welcome to a3fe’s documentation!

Contents:

• Getting Started
  • Installation
  • Quick Start
  • Quick Tips
• a3fe Design
  • Software Design
  • Algorithms
  • Some Notes on the Implementation
  • Units
• Guides
  • Preparing Input for a3fe
  • Running Standard Non-Adaptive Calculations
  • Customising Calculations
  • Running Fast Non-Adaptive Calculations
  • Running Adaptive Calculations
  • Analysis
  • Running Sets of Calculations
  • ABFE with Charged Ligands
• Warnings
• Change Log
  • 0.4.2
  • 0.4.1
  • 0.4.0
  • 0.3.6
  • 0.3.5
  • 0.3.4
  • 0.3.3
  • 0.3.2
  • 0.3.1
  • 0.3.0
  • 0.2.1
  • 0.2.0
  • 0.1.3
  • 0.1.2
  • v0.1.1
  • v0.1.0
• API Documentation
  • a3fe.configuration
  • a3fe.configuration.slurm_config
  • a3fe.configuration.engine_config
  • a3fe.configuration.system_prep_config
  • a3fe.run
  • a3fe.run._simulation_runner
  • a3fe.run.CalcSet
  • a3fe.run.Calculation
  • a3fe.run.Leg
  • a3fe.run.Stage
  • a3fe.run.LamWindow
  • a3fe.run.Simulation
  • a3fe.run.system_prep
  • a3fe.run._virtual_queue
  • a3fe.run._utils
  • a3fe.analyse
  • a3fe.analyse.analyse_set
  • a3fe.analyse.compare
  • a3fe.analyse.detect_equil
  • a3fe.analyse.mbar
  • a3fe.analyse.plot
  • a3fe.analyse.rmsd
  • a3fe.analyse.waters

Indices and tables

• Index

• Module Index

• Search Page