ArticleJournal of chemical information and modeling2023
Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Optimizing electroporation via pulse modulation: a molecular dynamics study.European biophysics journal : EBJ · 2025Article
- Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis.International journal of molecular sciences · 2024Article
- Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3.Molecules (Basel, Switzerland) · 2024Article
- Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks.Journal of chemical theory and computation · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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