Modules

Here is a list of all modules:

[detail level 12]

Public API	Classes and other symbols that are publicly accessible from user code
MD restraints	Apply restraints during MD integration
Library API	Classes and other symbols that are publicly accessible within the GROMACS library
Utility Modules	Modules with generic utility functions
Command Line Program Management (commandline)	Provides functionality for managing command line programs
Help Formatting for Online Help (onlinehelp)	Provides functionality for formatting help text for console and reStructuredText
Random engines and distributions (random)	Provides efficient and portable random generators and distributions
SIMD intrinsics interface (simd)	Provides an architecture-independent way of doing SIMD coding
Classes for table interpolation	Table interpolation from analytical or numerical input
Low-Level Utilities (utility)	Provides low-level utilities for error handling and other tasks
Testing Utilities (testutils)	Common helper classes and functions for writing tests using Google Test
Extensible Handling of Options (options)	Provides functionality for handling options
Analysis Modules	Modules used in analysis tools
Handling of writing new coordinate files	Provides basic functions to handle writing of new coordinate files
Correlation functions	Compute correlation functions and fit analytical functions to the result
Framework for Energy Analysis (energyanalysis)	Provides functionality for implementing energy analysis modules
Parallelizable Handling of Output Data (analysisdata)	Provides functionality for handling and processing output data from analysis
Parsing and Evaluation of Analysis Selections (selection)	Provides functionality for initializing and evaluating selections
Framework for Trajectory Analysis (trajectoryanalysis)	Provides functionality for implementing trajectory analysis modules
Modules for simulation functionality	Modules used in running simulations with mdrun
Spatial domain decomposition (for parallelization over MPI)	Manages the decomposition of the simulation volume over MPI ranks to try to distribute work evenly with minimal communication overheads
Ewald-family treatments of long-ranged forces	Computes energies and forces for long-ranged interactions using the Ewald decomposition. Includes plain Ewald, PME, P3M for Coulomb, PME for Lennard-Jones, load-balancing for PME, and supporting code
Interactive molecular dynamics (IMD)	Allows mdrun to interface with VMD via the interactive molecular dynamics (IMD) protocol
Interactions between lists of particles	Handles computing energies and forces for listed interactions
Implementation of mdrun utility functionality	This module contains code that implements general infrastructure for mdrun that does not suit any other module
The modular simulator	The modular simulator improves extensibility, adds Monte Carlo capabilities, promotes data locality and communication via interfaces, supports multi-stepping integrators, and paves the way for some task parallelism
Short-range non-bonded interaction module	Computes forces and energies for short-range pair-interactions based on the Verlet algorithm. The algorithm uses pair-lists generated at fixed intervals as well as various flavors of pair interaction kernels implemented for a wide range of CPU and GPU architectures
Non-bonded pair interactions	Implements non-bonded pair interaction functionality for NxM atom clusters
"Computational Electrophysiology" position swapping (swap)	Implements the "Computational Electrophysiology" protocol
Assigning simulation tasks to hardware (taskassignment)	Provides code that manages assignment of simulation tasks to hardware
Implementation of mdrun	This module contains code that implements mdrun
Integration test utilities	Functionality for testing mdrun as a whole
C++ standard library compatibility helpers.	Provide uniform interface to selected C++ standard library features
Accelerated weight histogram (AWH) method	Implements the "accelerated weight histogram" sampling method