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.