Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries

Bart M H Bruininks, Tsjerk A Wassenaar, Ilpo Vattulainen

Research output: Contribution to journalArticleAcademicpeer-review


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.

Original languageEnglish
Pages (from-to)3448-3452
Number of pages5
JournalJournal of Chemical Information and Modeling
Issue number11
Publication statusPublished - 12 May 2023
Externally publishedYes


  • computer simulation


Dive into the research topics of 'Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries'. Together they form a unique fingerprint.

Cite this