posted on 2023-05-12, 11:33authored byBart M. H. Bruininks, Tsjerk A. Wassenaar, Ilpo Vattulainen
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.