Molecular Dynamics Simulation of Thin Rods with an Analytical Interaction Potential

Following the Hamaker approach, we have derived an analytical interaction potential between two thin rods in arbitrary 3-dimensional arrangements by integrating the Lennard-Jones (LJ) 12-6 potential for interatomic interactions [1]. A similar potential is derived for the interaction between a thin rod and an LJ point particle. These potentials are implemented in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) as a user package to enable molecular dynamics simulations of rod systems, where an explicit solvent can also be included as an LJ liquid. Several applications of this new tool will be discussed, including the adhesion between slender rods and the lyotropic isotropic-nematic transition of a rod suspension. The analytical potentials for rods will find more applications in many systems involving slender objects, such as liquid crystals, polymers, colloids, cylindrical bacteria, carbon nanotubes, nanowires, filaments, and their bundles.