van der Straaten T.A., Kathawala G., Kuang Z., Boda D., Chen D.P., Ravaioli U., Eisenberg R.S., Henderson D.
University of Illinois, US
Keywords: comparitive simulation, electrolyte, pair correlation function
We use the pair correlation function as a benchmark calculation to compare three simulation methodologies -Equilibrium Monte Carlo, Molecular Dynamics, and Boltzmann Transport Monte Carlo. The three simulation approaches handle electrostatic boundary conditions and ion-water interactions, and evaluate electrostatic forces quite differently. The system simulated is a simple homogeneous electrolyte at equilibrium at concentrations of biological interest. Ions interact with each other via the electrostatic field and by either the standard Lennard-Jones interaction potential (LJ), or by a truncated form of LJ that mimics the ionic core repulsive part of the interaction potential. Ion-water interactions are represented by the primitive model, in which the water is modeled as a uniform dielectric medium. The pair correlation function has been calculated for monovalent and divalent electrolytes using both interaction potentials (standard LJ and truncated LJ). Initial results show good comparison between the three different simulations. We also show that the Boltzmann Transport Monte Carlo used in conjunction with the Particle-Particle-Particle Mesh (P3M) technique [2] allows the electrostatic forces to be resolved on a much coarser mesh while still recovering the correct pair correlation function, resulting in a considerable reduction in computational load.
Journal: TechConnect Briefs
Volume: 3, Technical Proceedings of the 2003 Nanotechnology Conference and Trade Show, Volume 3
Published: February 23, 2003
Pages: 447 - 451
Industry sector: Medical & Biotech
Topic: Biomaterials
ISBN: 0-9728422-2-5