Gromacs
2024.4
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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 |