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GROMACS 2025.4-Ubuntu_2025.4_1 documentation
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  • Installation guide
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    • Getting started
      • Flow Chart
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    • Answers to frequently asked questions (FAQs)
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    • Command-line reference
      • molecular dynamics simulation suite
      • gmx anaeig
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      • gmx helixorient
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      • gmx trajectory
      • gmx trjcat
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      • gmx tune_pme
      • gmx vanhove
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      • Selection syntax and usage
    • Terminology
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  • Short How-To guides
    • Beginners
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    • Carbon Nanotube
    • Visualization Software
    • Extracting Trajectory Information
    • External tools to perform trajectory analysis
    • Plotting Data
    • Micelle Clustering
  • Reference Manual
    • Preface and Disclaimer
    • Introduction
    • Definitions and Units
    • Algorithms
      • Periodic boundary conditions
      • The group concept
      • Molecular Dynamics
      • Shell molecular dynamics
      • Constraint algorithms
      • Simulated Annealing
      • Stochastic Dynamics
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      • Free energy calculations
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    • Interaction function and force fields
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      • Restraints
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      • Force field
    • Topologies
      • Particle type
      • Parameter files
      • Molecule definition
      • Constraint algorithms
      • pdb2gmx input files
      • File formats
      • Force field organization
    • File formats
    • Special Topics
      • Free energy implementation
      • Potential of mean force
      • Non-equilibrium pulling
      • Collective variables: the pull code
      • Adaptive biasing with AWH
      • Enforced Rotation
      • Electric fields
      • Computational Electrophysiology
      • Calculating a PMF using the free-energy code
      • Removing fastest degrees of freedom
      • Viscosity calculation
      • Shear simulations
      • Tabulated interaction functions
      • Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface
      • MiMiC Hybrid Quantum Mechanical/Molecular Mechanical simulations
      • Using VMD plug-ins for trajectory file I/O
      • Interactive Molecular Dynamics
      • Embedding proteins into the membranes
      • Applying forces from three-dimensional densities
      • Collective Variable simulations with the Colvars module
      • Using PLUMED
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    • Run parameters and Programs
    • Analysis
      • Using Groups
      • Looking at your trajectory
      • General properties
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      • Hydrogen bonds
      • Protein-related items
      • Interface-related items
    • Some implementation details
    • Averages and fluctuations
    • Bibliography
  • gmxapi Python package
    • Full installation instructions
    • Using the Python package
    • gmxapi Python module reference
  • (Non-)Bonded LIBrary (NB-LIB) API
    • Guide to Writing MD Programs
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    • Development-time tools
      • Using Doxygen
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        • GitLab CI Pipeline Execution
      • Source tree checker scripts
      • Automatic source code formatting
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      • Physical validation
    • Known issues relevant for developers
  • Doxygen documentation
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