Molecular Dynamics Simulations of Zinc Ions in Water Using CHARMM

Abstract

Molecular Dynamics simulations of a zinc ion with 123 and 525 TIP3P-water molecules were carried out with CHARMM using two different Lennard-Jones parameter sets for the Zn²⁺ ion. The results were compared to published experimental and simulation data. Good agreement was found for radial distribution functions, number of hydrogen bonds, and diffusion coefficients. Experimental radial distribution functions were better reproduced by the original CHARMM22 parameter set than by the parameter set modified by Stote and Karplus. Diffusion coefficients were found to depend on the system size rather than on the parameter set used and were better reproduced by the larger systems. The divalent zinc ion exerts a strong influence on its hydration shell as indicated by the high first peak of the radial distribution function. Water molecules in the vicinity of the zinc ion show a slight deformation of the O-H bond length and of the H-O-H bond angle as compared to pure water. No water molecules from the first hydration shell were exchanged during 1 ns of MD simulation.