5. API documentation

The gromacs package makes Gromacs tools available via thin Python wrappers, which are generated in gromacs.tools and made available in the top-level name space gromacs. The functionality to generate the tool wrappers resides in the core modules.

Building blocks to solve commonly encountered tasks related to set-up and running of simulations are collected as building blocks.

• 5.1. Gromacs core modules
  • 5.1.1. gromacs.core – Core functionality
  • 5.1.2. gromacs.config – Configuration for GromacsWrapper
  • 5.1.3. gromacs.environment – Run time modification of behaviour
  • 5.1.4. gromacs.formats – Accessing various files
  • 5.1.5. gromacs.utilities – Helper functions and classes
  • 5.1.6. analysis.collections – Handling of groups of simulation instances
  • 5.1.7. gromacs.tools – Gromacs commands classes
• 5.2. Gromacs building blocks
  • 5.2.1. gromacs.cbook – Gromacs Cook Book
  • 5.2.2. gromacs.setup – Setting up a Gromacs MD run
  • 5.2.3. gromacs.scaling – Partial tempering
  • 5.2.4. gromacs.qsub – utilities for batch submission systems
  • 5.2.5. gromacs.run – Running simulations