.. _algorithms:

Algorithms
==========

In this chapter we first give describe some general concepts used in
|Gromacs|: *periodic boundary conditions* (sec. :ref:`pbc`) and the *group
concept* (sec. :ref:`groupconcept`). The MD algorithm is described in
sec. :ref:`MD`: 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. :ref:`EM`. 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 :ref:`ff`. 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 :ref:`analysis`.

.. toctree::
   :maxdepth: 2

   algorithms/periodic-boundary-conditions
   algorithms/group-concept
   algorithms/molecular-dynamics
   algorithms/shell-molecular-dynamics
   algorithms/constraint-algorithms
   algorithms/simulated-annealing
   algorithms/stochastic-dynamics
   algorithms/brownian-dynamics
   algorithms/energy-minimization
   algorithms/normal-mode-analysis
   algorithms/free-energy-calculations
   algorithms/replica-exchange
   algorithms/essential-dynamics
   algorithms/expanded-ensemble
   algorithms/parallelization-domain-decomp