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.
This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual.
This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from.
- Known issues affecting users of GROMACS
- Getting started
- System preparation
- Managing long simulations
- Answers to frequently asked questions (FAQs)
- Force fields in GROMACS
- Molecular dynamics parameters (.mdp options)
- Useful mdrun features
- 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
- Command-line reference
- Environment Variables
- Floating point arithmetic
- Security when using GROMACS
- Policy for deprecating GROMACS functionality