I have a working non-equilibrium molecular dynamics model of MgO. I first find the equilibrium positions of the atoms in the lattice and then introduce a temperature by assigning initial velocities in random directions for each atom. An equation relating atomic velocity and temperature is [itex]mv^2=3k_BT[/itex] where k_b is the boltzmann constant. So for example, oxygen with mass=2.66*10^-26 kg, and with T=2000K each oxygen is assigned a velocity v=1766 m/s. Running the simulation, however, I observe that as the atoms move out of their T=0K equilibrium positions their velocity decreases until they begin bouncing off zero as the atoms bounce off one another. When the system is in a steady state of vibration the average temperature and atomic velocity in the lattice becomes about 1/2 of the initially assigned temperature, ~880 m/s and ~1000 K in this case. This seems to be a transfer of kinetic energy into potential energy from moving out of the bottom of the potential energy well, but I'm not sure? Is this associated with a particular concept or phenomenon? Latent heat? The decrease in velocity is roughly 1/2 for all temperatures so I don't think it is related to specific heat. Where is the energy going? Is the actual temperature of the lattice 1000K or 2000K? How do I determine temperature in such a case?