Constant pressure-constant temperature molecular dynamics: a correct constrained NPT ensemble using the molecular virial

In the present work we introduce a simple, Nose-Hoover style isothermal-isobaric molecular dynamics method for systems with holonomic molecular constraints and the molecular representation of the virial. We prove, using the non-Hamiltonian dynamics approach, recently developed by Tuckerman et al. [1999, Europhys. Lett., 45, 149], that the phase space distribution, generated by our equations, samples the desired ensemble under all circumstances. We also write down the explicit reversible integrator for our equations. This integrator has been implemented in the last version of the DLProtein program