Andersen's canonical-ensemble molecular dynamics for molecules with constraints

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Abstract
The heat batch coupling of Andersen leading to canonical ensemble molecular dynamics (MD) simulations is extended to fully or partially rigid molecules within a description using cartesian coordinates for the atoms. In particular, we propose a new method to sample cartesian velocities of the individual atoms in which the use of generalized coordinates is completely avoided. We also give a straightforward implementation of this method when it is combined with a usual MD program integrating the cartesian equations of motion. For systems consisting of partially rigid molecules, this method is particularly appropriate for establishing, in an efficient way, the thermal equilibrium among all the inter-intramolecular modes explicitly considered.