Quaternions as a tool for the analysis of molecular systems

Quaternions are generalized complex numbers and represent rotations in space as ordinary complex numbers represent rotations in a plane. In the context of molecular dynamics (MD) simulations they have been ‘rediscovered’ for the integration of the rotational equation of motion of rigid molecules since they allow one to write down these equations in a singularity-free form. In this paper applications to the analysis of molecular systems are described.