I've noticed some authors scale the mass of particles in molecular dynamics simulations while leaving the force field parameters the same in order to achieve materials of different densities. Does this not impact the thermodynamic properties derived from the dynamics of the system? I would imagine the phase space would look very different with an artificial and arbitrary mass/force field combination, but I may be wrong.
Total energy has independent contributions from kinetic energy and potential energy. The kinetic energy component is determined by temperature and is not affected by particle mass (although obviously velocities will be affected). The potential energy components also do not depend on mass (e.g. Coulombic effects). It's somewhat counter-intuitive but the thermodynamic properties of the system will be not be changed. The dynamical properties will be changed, but these are two different issues.
Since someone asked for an example, here's a publication that I believe should be accessible to anyone, with or without journal access:
In this case the authors are interested in speeding up a simulation by slowing down hydrogen motions which would allow bigger time steps. Right in the abstract they claim that this will not change the thermodynamic properties of the system:
In principle introducing dummy atoms and increasing hydrogen mass do not influence thermodynamical properties of the system and dynamical properties are shown to be influenced only to a moderate degree.
For this answer I have in mind typical molecular dynamics forcefields using for macromolecules but if you were using some sort of astronomical forcefield with gravitational effects then the answer would be different.