Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency

From a specific definition of the roto-translational (external) and intramolecular (internal) coordinates, a constrained dynamics algorithm is derived for removing the roto-translational motions during molecular dynamics simulations, within the leap-frog integration scheme. In the paper the theoretical basis of this new method and its statistical mechanical consistency are reported, together with two applications.