Molecular dynamics (MD) is a major part of FAH. Most (but not all) of the FAH cores are MD engines. The basic idea behind MD is to simulate reality by following how atoms would move around, driven by Newton's equations. This is much like trying to predict how a pool game would go by simulating how the balls move around the table. This only works if you know what are the forces being put on the balls and this is the same in MD -- we need to know the forces that the atoms exert on each other.
One of the key assets of MD is that it can predict kinetics, i.e. not just what the final outcome would be (thermodynamics) but how it happened. This is particularly important for studying protein folding and protein misfolding, as this is precisely what we're interested in. However, there are other cases where we care purely about the end in a statistical manner (eg out of 1,000,000 drug molecules, what fraction would bind to this protein?). While there are other methods that could be used in this case (eg Monte Carlo methods), MD can often be more efficient than Monte Carlo (MD has a better "move set" than MC and MD codes tend to be better optimized and computationally efficient).
There are lots of other issues to deal with and MD Is just one of them. I'll talk about other issues in the future. In particular, it's important to ask where do the forces come from that we use. This brings up the question of force fields, which I'll leave for a post in the future.