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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
    • Setting up your environment
    • Flowchart of typical simulation
    • Important files
    • Tutorial material
    • Background reading
  • Non-bonded cut-off schemes
    • Non-bonded scheme feature comparison
    • Performance
    • How to use the Verlet scheme
    • Further information
  • Useful mdrun features
    • Re-running a simulation
    • Running a simulation in reproducible mode
    • Running multi-simulations
    • Controlling the length of the simulation
    • Running a membrane protein embedding simulation
  • Getting good performance from mdrun
    • Hardware background information
    • GROMACS background information
    • Running mdrun within a single node
    • Running mdrun on more than one node
    • Controlling the domain decomposition algorithm
    • Finding out how to run mdrun better
    • Running mdrun with GPUs
    • Running the OpenCL version of mdrun
  • Molecular dynamics parameters (.mdp options)
    • General information
  • File formats
    • Summary of file formats
    • File format details
  • Command-line reference
    • Command-line interface and conventions
    • Commands by name
    • Commands by topic
    • Special topics
    • Command changes between versions
  • Environment Variables
    • Output Control
    • Debugging
    • Performance and Run Control
    • OpenCL management
    • Analysis and Core Functions

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