Gromacs  2016.4
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Modules for simulation functionality
+ Collaboration diagram for 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.
 "Computational Electrophysiology" position swapping (swap)
 Implements the "Computational Electrophysiology" protocol.
 Implementation of mdrun
 This module contains code that implements mdrun.
 Integration test utilities
 Functionality for testing mdrun as a whole.