We show that in the molecular dynamics simulation of systems where the molecules are subjected to holonomic constraints the isobaric-isothermal (NPT) techniques can be applied by scaling in space the atomic coordinates rather than the molecular center of mass, as has been customary until now. The correct constrained distribution function is obtained by applying the original Andersen transformation or equivalently the Hoover-type NPT equations of motion. The latter set of equations are shown to be derived from an underlying Lagrangian. The atomic scaling is preferred to the molecular one when simulating large molecules since molecular metastabilities are more easily overcome. However, also for systems composed of small molecules, the approach can be interesting since in this way cell rotations are automatically avoided.