Molecular dynamics of rigid molecules

We develop a Hamiltonian formalism for an ensemble of rigid molecules in the quaternionic representation. In the quaternionic language different symmetries of the rigid top dynamics acquire a simple and natural expression. Subsequently we describe the coupling of the ensemble of rigid molecules to a thermostat. The isothermal molecular dynamics is defined by introducing additional pseudofriction coefficients, according to a generalized Nosé–Hoover prescription.