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.