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 part of the documentation.

Please reference this documentation as https://doi.org/10.5281/zenodo.3243834.

To cite the source code for this release, please cite https://doi.org/10.5281/zenodo.3243833.

• Getting started
  • Setting up your environment
  • Flowchart of typical simulation
  • Important files
  • Tutorial material
  • Background reading
• System preparation
  • Steps to consider
  • Tips and tricks
• Managing long simulations
  • Appending to output files
  • Backing up your files
  • Extending a .tpr file
  • Changing mdp options for a restart
  • Restarts without checkpoint files
  • Are continuations exact?
  • Reproducibility
• Answers to frequently asked questions (FAQs)
  • Questions regarding GROMACS installation
  • Questions concerning system preparation and preprocessing
  • Questions regarding simulation methodology
  • Parameterization and Force Fields
  • Analysis and Visualization
• Force fields in GROMACS
  • AMBER
  • CHARMM
  • GROMOS
  • OPLS
• Non-bonded cut-off schemes
  • Non-bonded scheme feature comparison
  • Performance
  • How to use the Verlet scheme
  • Further information
• Command-line reference
  • Command-line interface and conventions
  • Commands by name
  • Commands by topic
  • Special topics
  • Command changes between versions
• Molecular dynamics parameters (.mdp options)
  • General 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
  • Work distribution by parallelization in GROMACS
  • Parallelization schemes
  • Running mdrun within a single node
  • Running mdrun on more than one node
  • Approaching the scaling limit
  • Finding out how to run mdrun better
  • Running mdrun with GPUs
  • Running the OpenCL version of mdrun
  • Performance checklist
• Common errors when using GROMACS
  • Common errors during usage
  • Errors in pdb2gmx
  • Errors in grompp
  • Errors in mdrun
• Command-line reference
  • Command-line interface and conventions
  • Commands by name
  • Commands by topic
  • Special topics
  • Command changes between versions
• Terminology
  • Pressure
  • Periodic boundary conditions
  • Thermostats
  • Energy conservation
  • Average structure
  • Blowing up
  • Diagnosing an unstable system
  • Molecular dynamics
  • Force field
• Environment Variables
  • Output Control
  • Debugging
  • Performance and Run Control
  • OpenCL management
  • Analysis and Core Functions
• Floating point arithmetic
• Security when using GROMACS
• Policy for deprecating GROMACS functionality