Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12–6 Lennard-Jones (LJ) term plus an electrostatic potential, is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models, and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work, we…

• UO
  University of Florida
• NI
  National Institutes of Health