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GROMACS 2025.1 documentation

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Downloads
Release notes
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Installation guide
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- Installation guide for exotic configurations
User guide
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- Known issues affecting users of GROMACS
- Getting started
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  - Flow Chart
- System preparation
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- Managing long simulations
- Answers to frequently asked questions (FAQs)
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- Force fields in GROMACS
- Molecular dynamics parameters (.mdp options)
- Useful mdrun features
- Getting good performance from mdrun
- Common errors when using GROMACS
- Command-line reference
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- Terminology
- Environment Variables
- Floating point arithmetic
- Security when using GROMACS
- Policy for deprecating GROMACS functionality
Short How-To guides
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Reference Manual
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- Preface and Disclaimer
- Introduction
- Definitions and Units
- Algorithms
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- Interaction function and force fields
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- Topologies
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- File formats
- Special Topics
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- Run parameters and Programs
- Analysis
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- Some implementation details
- Averages and fluctuations
- Bibliography
gmxapi Python package
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(Non-)Bonded LIBrary (NB-LIB) API
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- Guide to Writing MD Programs
C++ API
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- Public C++ API
Developer Guide
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- Contribute to GROMACS
- Codebase overview
- Build system overview
- Change Management
- Relocatable binaries
- Documentation generation
- Style guidelines
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- Development-time tools
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  - Using Doxygen
  - Change Management
  - Automation and Infrastructure
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    - GitLab CI Pipeline Execution
  - Source tree checker scripts
  - Automatic source code formatting
  - Unit testing
  - Physical validation
- Known issues relevant for developers
Doxygen documentation

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Removed functionality¶

Removed GMX_SCSIGMA_MIN environment variable¶

This was used to reproduce free-energy soft-core behavior of GROMACS versions before 4.5.

Deprecated functionality

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Removed functionality
- Removed GMX_SCSIGMA_MIN environment variable