section_Ligand_Dynamics_and_Free__.tex

\section{Ligand Dynamics and Free Energy Calculations}
  
Simulation based approaches for analyzing ligand-protein interactions have the potential to fully account for the dynamics of the ligand, protein, and water system.  Molecular dynamics simulation is a powerful tool for computing free energies as long as the system can be properly parameterized and the simulation code adapted and analyzed to implement the desired free energy method.