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. If you have questions not answered by these resources, please visit the GROMACS users forum and search for a potential answer or ask a question from the community.

Please reference this documentation as https://doi.org/10.5281/zenodo.7586765.

To cite the source code for this release, please cite https://doi.org/10.5281/zenodo.7586780.

• Known issues affecting users of GROMACS
  • Unable to compile with CUDA 11.3
  • Verlet buffer underestimated for inhomogeneous systems
  • Verlet buffer underestimated when using only r^-12 potentials
  • The deform option is not suitable for flow
  • Build is fragile with gcc 7 and CUDA
  • SYCL build unstable when using oneAPI with LevelZero backend
  • Unable to build with CUDA 11.5-11.6 and GCC 11 on Ubuntu 22.04
  • Expanded ensemble does not checkpoint correctly
• 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
• Molecular dynamics parameters (.mdp options)
  • General information
• Useful mdrun features
  • Re-running a simulation
  • Running a simulation in reproducible mode
  • Halting running simulations
  • Running multi-simulations
  • Controlling the length of the 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