Mass Scaling of 3-site Water. In MD simulations of biomolecules, the viscosity of the solvent is a major determinant of the speed not just of diffusion but also of conformational changes, and thus of the sampling efficiency. Scaling the masses of solvent molecules 6 by a factor f 2 , i.e., m ′ = f 2 m, changes the solvent viscosity by a factor f , η ′ = f η.