Molecular Dynamics algorithms like Gromacs and AMBER aim to simulate atomistic mechanisms of biological macromolecules.
This video shows a good example of a resulting video from such a simulation for the CmAAT1 Enzyme, CmAAT1-Hex-aCoA complex. Much more data such as energy values and electrostatic interactions is available from the simulation, but that's not as pretty as the video!
There are also telltale signs of active regions of crystal structures. Software like Consurf can show conserved residues. This implies possible biochemically important features like key structural or enzymatic residues, areas of a protein. The image below is from the consurf gallery and is based on the crystal structure 3COQ. Pink is areas of conservation. It therefor appears that those residues are involved in binding DNA.
Consurf is only one of many tools for identifying key residues. After these residues are identified, mutant knockouts of the protein can be made to see exactly how the function of the protein is altered. From that, a fairly good mechanistic model can emerge.
"Can we know..."
The word "know" is a philosophically ambiguous word and I've gathered that scientists generally tend to avoid it. This is particularly true when it comes to the simulation side of things. It is generally best to regard MD simulations as an approximation of what happens.