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.14016613.
To cite the source code for this release, please cite https://doi.org/10.5281/zenodo.14016590.
- Known issues affecting users of GROMACS
- Unable to compile with CUDA 11.3
- The deform option is not suitable for flow
- 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
- FFT errors with NVIDIA RTX 40xx-series GPUs and CUDA 11.7 or earlier
- “Cannot find a working standard library” error with ROCm Clang
- Expanded ensemble does not checkpoint correctly
- Compiling with GCC 12 on POWER9 architectures
- Launching multiple instances of GROMACS on the same machine with AMD GPUs
- 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
- Avoiding communication for constraints
- Finding out how to run mdrun better
- Running mdrun with GPUs
- Running the OpenCL version of mdrun
- Running SYCL 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