# AlgorithmsΒΆ

In this chapter we first give describe some general concepts used in
GROMACS: *periodic boundary conditions* (sec. Periodic boundary conditions) and the *group
concept* (sec. The group concept). The MD algorithm is described in
sec. Molecular Dynamics: first a global form of the algorithm is given, which is
refined in subsequent subsections. The (simple) EM (Energy Minimization)
algorithm is described in sec. Energy Minimization. Some other algorithms for
special purpose dynamics are described after this.

A few issues are of general interest. In all cases the *system* must be
defined, consisting of molecules. Molecules again consist of particles
with defined interaction functions. The detailed description of the
*topology* of the molecules and of the *force field* and the calculation
of forces is given in chapter Interaction function and force fields. In the present chapter we
describe other aspects of the algorithm, such as pair list generation,
update of velocities and positions, coupling to external temperature and
pressure, conservation of constraints. The *analysis* of the data
generated by an MD simulation is treated in chapter Analysis.

- Periodic boundary conditions
- The group concept
- Molecular Dynamics
- Shell molecular dynamics
- Constraint algorithms
- Simulated Annealing
- Stochastic Dynamics
- Brownian Dynamics
- Energy Minimization
- Normal-Mode Analysis
- Free energy calculations
- Replica exchange
- Essential Dynamics sampling
- Expanded Ensemble
- Parallelization
- Domain decomposition