Gromacs
2024.3
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Modules used in running simulations with mdrun.
Modules | |
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. | |