Monte Carlo simulation of several biologically relevant molecules and zwitterions in water

In this work, we study the hydration free energies of butane, zwitterionic alanine, valine, serine, threonine, and asparagine, and two neuraminidase inhibitors by means of Monte Carlo (MC) simulation. The solute molecule, represented in the form of distributed multipoles and modified 6–12 potential, was varied from a non-interacting ‘ghost’ molecule to its full potential functions in TIP4P water. Intermediate systems with soft-core solute–solvent interaction potentials are simulated separately and then subjected to Bennett’s Acceptance ratio (BAR) for the free energy calculation. Hydration shells surrounding the solute particles were used to assess the quality of potential functions.