Molecular Dynamics Simulation of the Metal-Organic Framework UiO-66 in NAMD Under Periodic Boundary Conditions

The metal-organic framework UiO-66 is a material studied by molecular simulation for applications such as drug storage and contaminant adsorption, among other uses. Here, the implementation of the unit cell of UiO-66 is demonstrated for molecular dynamic simulations in the NAMD software using full-periodic and semi-periodic boundary conditions, with full detail for reproducibility. The method builds a PDB file (coordinates) from experimental data and a PFS file (structure) using Topotools for a given force field, with appropriate treatment of the periodic boundary conditions. Structural parameters of the material (lattice constant, internal bonds, angles, and dihedral angles) verify the implementation. For the semi-periodic system, lack of structure in the surface is detected compared to the bulk of the material.