Fig 1. The chemical potential simulation.

The protein is placed in a simulation box big enough to accommodate 3 layers of solvent—water in this case. The simulation is started with a high chemical potential and solvent molecules rapidly fill the box and occupy (a) all possible cavities at the surface and deep within the protein. As the chemical potential is lowered, not much happens until this free energy reaches a critical level that is capable of destroying the solvent cohesion and the system goes through a phase transition that evacuates the bulk solvent and most of the protein-bound solvent, exposing high affinity (b) binding sites. Continuing to lower the chemical potential further reveals the extremely high affinity (c) binding sites. A plot of the number of fragments in the simulation box versus the chemical potential shows the abrupt transition when the bulk solvent is evaporated from the cell. The charged state of the catalytic aspartates in HIV protease (Asp = charged, Ash = neutral) does not change the phase transition.