User guide

This guide provides

• material introducing GROMACS
• practical advice for making effective use of GROMACS.

For getting, building and installing GROMACS, see the Installation guide. For background on algorithms and implementations, see the reference manual.

• Getting started
  • Setting up your environment
  • Flowchart of typical simulation
  • Important files
  • Tutorial material
  • Background reading
• Non-bonded cut-off schemes
  • Non-bonded scheme feature comparison
  • Performance
  • How to use the Verlet scheme
  • Further information
• Useful mdrun features
  • Re-running a simulation
  • Running a simulation in reproducible mode
  • Running multi-simulations
  • Controlling the length of the simulation
  • Running a membrane protein embedding simulation
• Getting good performance from mdrun
  • Hardware background information
  • GROMACS background information
  • Running mdrun within a single node
  • Running mdrun on more than one node
  • Controlling the domain decomposition algorithm
  • Finding out how to run mdrun better
  • Running mdrun with GPUs
  • Running the OpenCL version of mdrun
• Molecular dynamics parameters (.mdp options)
  • General information
• File formats
  • Summary of file formats
  • File format details
• Command-line reference
  • Command-line interface and conventions
  • Commands by name
  • Commands by topic
  • Special topics
  • Command changes between versions
• Environment Variables
  • Output Control
  • Debugging
  • Performance and Run Control
  • OpenCL management
  • Analysis and Core Functions