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 part of the documentation.
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.
- Getting started
- System preparation
- Managing long simulations
- Answers to frequently asked questions (FAQs)
- Force fields in GROMACS
- Command-line reference
- 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
- Terminology
- Environment Variables
- Floating point arithmetic
- Security when using GROMACS
- Policy for deprecating GROMACS functionality