Charged binding calculations

Authored by Gabriel Rocklin, last updated June 15 2014

Free energy calculations can be used to calculate free energies for processes involving a change in net charge, such as protonation of a side chain, binding of a charged ligand, or transfer of an ion from the gas phase to the solution phase. For a long time, it was uncertain whether these processes would introduce artifacts due to the net charge of the system, but these artifacts are now reasonably well understood and analytical methods are available to correct for these artifacts.