User guideΒΆ
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
- System preparation
- Managing long simulations
- Answers to frequently asked questions (FAQs)
- Force fields in GROMACS
- Non-bonded cut-off schemes
- Command-line reference
- Molecular dynamics parameters (.mdp options)
- Useful mdrun features
- Getting good performance from
mdrun - Common errors when using GROMACS
- File formats
- Terminology
- Environment Variables
- Floating point arithmetic