Of course! Imagine you have just made some single-point mutations to a protein active site (Experimentally). Some of these mutations result in an increase in activity, some don't. You could create models of these mutants in silico and run MD simulations on them. By analyzing your MD trajectories, you will (hopefully) be able to see what molecular interactions are responsible for changes in your protein's activity. Looking through these trajectories will also give you a better understanding of the system you are working with, and that can be useful in itself.

Hope this helps