Charged binding calculations

Authored by Gabriel Rocklin, last updated June 15 2014

Overview

Many thermodynamically interesting processes involve ions changing chemical environment, such as the transfer of an ion from the gas phase to the solvated phase, the protonation of a protein side chain, or the binding of a charged ligand. Free energy simulations of these processes can be done in two ways: (1) the same simulated system can be used for both chemical environments, such as when a charged ligand is "pulled" from a protein binding site into the bulk solvent, or (2) different simulated systems can be used for different chemical environments, such as when a charged ligand is alchemically decoupled from its own "free in solution" box and alchemically inserted/coupled into the protein binding site in a different simulated system. In both cases, the computed free energies can depend on details of the calculation setup, such as the boundary conditions applied at the edge of the explicit solvent system (periodic, implicit solvent, or vacuum), the size of the periodic unit cell, and even completely arbitrary details of the solvent molecular topology.

These dependences on setup parameters are referred to as "finite size effects" because they are caused by the finite and extremely small size of the simulated system/periodic unit cell relative to the macroscopic size of the experimental system. Finite size effects are basically computational artifacts because they contribute to the simulated free energy change but not to a bulk experimental measurement. It is thus desirable to remove these free energy contributions before comparing simulated free energy results with experimental results. The conventional way to do this is to convert the raw simulation results (which are specific to the particular choices of boundary condition, system size, molecular topology, etc) into corrected