GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds, to millions of particles. See www.gromacs.org for more information.

This documentation generated by Doxygen is (mostly) extracted from the source code, and provides documentation for understanding the source code. The documentation can be generated with different levels of details. This documentation has been generated to include all documentation, including internal functions and classes used for internal implementation purposes.

The main audience for this level of detail are people who want to understand detailed implementation of some area, or try to find some specific function within the library. If you are overwhelmed by the amount of details, the library API documentation skips functions not meant to be used outside a single module.

Currently, only parts of the code are documented here. The following pages give an overview of some of the topics that are documented:

• Framework for trajectory analysis
  Provides an overview of the framework that the GROMACS library provides for writing (trajectory) analysis tools.
• Help formatting
  Provides an overview of the formatting markup available in help texts.
• Using GROMACS as a library
  Provides general guidance for writing software that uses the GROMACS library.
• Wrapper binary implementation
  Provides an overview of how the gmx wrapper binary is implemented.
• Logging
  Documentation for logging and status output (for now, within mdrun).
• Single-instruction Multiple-data (SIMD) coding
  Documentation about the new SIMD module that makes it possible to write highly accelerated CPU code that is still portable.
• The NxM atom-cluster non-bonded algorithm
  Documentation about the non-bonded module which uses NxM atom clusters.
• The accelerated weight histogram method (AWH)
  Documentation about the accelerated weight histogram (AWH) method, which is used for accelerating sampling along reaction coordinates.
• mdrun modules
  Documentation for work-in-progress modularization of parts of mdrun, that should make it easier to implement additional features as add-ons on top of a common interface.
• Using reference data in C++ tests
  Documentation for writing tests that use reference data generated by the same test.
• The modular simulator
  Documentation of the modular simulator approach.
• Module dependency graph
  Automatically generated module dependency graph.

This list will hopefully expand over time.