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.
You bring up an excellent point, papaf. The accuracy of the empirical force fields used in molecular dynamics simulation engines (such as Gromacs) is a hotly debated topic. Even without quantum computing the issue can be addressed with conventional computers that perform quantum mechanical calculations on interacting molecular fragments. The forces calculated from quantum mechanics can then be compared with those calculated from molecular dynamics force fields (as an example see Sherrill et al. http://onlinelibrary.wiley.com/doi/10.1002/jcc.21226/full ). Such studied have shown that current force fields fail to model certain chemical interactions and need improved. Specifically, the underlying functional forms used to model molecular forces need revised.
Currently such investigations are limited in scope by the large computational resources required to perform a single quantum mechanical calculation on a molecular fragment. With quantum computers, tens of thousands of such calculations could be performed and the results could be used to optimize new molecular force fields through multivariate regression.
Nice to see another GT person on HN! (Did my undergrad there.) Have you worked with Dr. Sherrill? It's funny you mention him; I was actually reading one of his presentations on electron-electron correlation last night.
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.