In our lab we use QM/MM Molecular Dynamics simulations to study how enzymes work.
Specifically, we first investigate the reaction in aqueous solution and then compare the reaction mechanism to the one in the enzyme. Our main method to study the influence of the enzyme on the reaction mechanism is the Mean Reaction Force (MRF).
If you got interested we are continously looking for new motivated students to perform paid undergraduate thesis in our lab. You can contact me here ...
As an example of ongoing research the picture above shows the transition state of our recent published paper on the Prolyl cis-trans isomerization reaction catalyzed by Pin1 in JPCB (DOI:10.1021/jp307946h).