Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries

Abstract

In molecular simulations, periodic boundary conditions are typically used to avoid surface effects occurring at the boundaries of the simulation box. A consequence of this is that molecules and assemblies may appear split over the boundaries. Broken molecular assemblies make it difficult to interpret, analyze, and visualize molecular simulation data. We present a general and fast algorithm that repairs molecular assemblies that are broken due to periodic boundary conditions. The open source method presented here, MDVWhole, works for all translation-only crystallographic periodic boundary conditions. The method consumes little memory and can fix the visualization of the assembly of millions of particles in a few seconds. Thus, it is suitable for processing both single simulation frames and long trajectories with millions of points.