Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries

J Chem Inf Model. 2023 Jun 12;63(11):3448-3452. doi: 10.1021/acs.jcim.2c01574. Epub 2023 May 12.


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.

PMID:37171034 | PMC:PMC10268952 | DOI:10.1021/acs.jcim.2c01574