Unbreaking Assemblies in Molecular Simulations with Periodic Boundaries.
J Chem Inf Model
; 63(11): 3448-3452, 2023 06 12.
Article
em En
| MEDLINE
| ID: mdl-37171034
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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Base de dados:
MEDLINE
Assunto principal:
Simulação por Computador
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article