Molecular dynamics simulation using quaternions (Q1088369)

Quaternion representations of rotations and molecular rotational motions are used to provide differential equations free of numerical singularity difficulties associated with other (e.g. Euler angle) formulations. It is shown how the classical rotational motion may be described to advantage by second order differential equations soluble by similar numerical methods to those used for the concurrent translational motion. An outline of the application of the methods to an extensive molecular dynamics simulation of water is given. Predictor corrector integration minimizes the time consuming calculation of torques and forces at each step. Required position/orientation quantities are easily evaluated with the chosen variables and the method appears to enable a larger time step size to be used for the same kinetic temperature drift.