Hi Lammpers:

I am trying to simulate what I think of as dynamic properties. Here is my example: I have a periodic boundary condition box full of polymer. Chains of 10 monomers each. I am dropping the temperature by 0.1 instantaneously, from 0.7 to 0.6 say. I want to watch the energy dip as the systems relaxes into the lower temperature. I expect some sort of exponential decay in energy. I cannot seem to get away from the damping qualities of the integrator (I use npt here). The damping drives the system. Whatever damp I choose: 10, 100, 200 in each case the energy is driven by the wavelength chosen by the damp parameter.

The problem is the barostat and thermostat drive the dynamics, and the only statistics I can rely on are the ones derived from properties associated from the equilibrium.

One question is, how do I get away from the stat damping?

More deeply, I seem to be at a point here where questions of dynamics (pre eqilibrium) just cannot be answered by molecular dynamics?

Thanks for your thoughts.