My understanding of these things is that the dynamics of the real world are not easily measurable at this scale. An alternative is to simulate using using packages such as Gromacs:

  http://www.gromacs.org/About_Gromacs

These packages are truly incredible but use relatively crude approximations and are in wide use. It is possible to get a decent paper out that uses a simulation as evidence to support an idea.

The aim of my question was to see if chemically accurate simulations come up with significantly different answers or to see if the current way of doing things is a good enough approximation.