``Molecular Mechanics'' refers to computational techniques which use classical mechanics to analyze the structure and dynamics of molecular systems including biological macromolecules, organic compounds, polymers, and materials. These systems are composed of atoms which are treated as classical particles, whose interactions are described by simple two-, three-, and four-body potential energy functions. This classical forcefield-based approach is a great simplification over quantum chemistry, which describes systems in terms of nuclei, electrons, and orbitals. This simplicity allows molecular mechanics to be applied to much larger systems than can be studied by ab initio methods. Tremendous improvements in computer power and computational methodology have accelerated the pace towards simulation of larger and larger systems, so that today simulations of a million particles is possible. Such advances have also enabled researchers to obtain much greater information from their simulations: more accurate calculation of physical and chemical properties or simulations of much longer dynamical processes.
The simplest calculation in molecular mechanics is a calculation of the potential energy of the system, which is performed by summing the numerous energy terms for the given conformation of the system using the given set of potential energy functions and parameters. Optimizing the structure of a system can be done by ``energy minimization'' which improves the conformation by reducing the gradients and the energy of the system. A great deal more information about a system can be obtained from molecular dynamics simulations. In these calculations, the motions of the particles are followed by calculating the forces from the forcefield and, from this, the accelerations and velocities. Careful control of the energy and temperature of the system ensures that the conformations produced form a statistical ensemble, from which thermodynamic and other properties can be calculated.