Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

• Published in: Nature communications Vol. 13; no. 1; pp. 68 - 12
• Main Authors: Grünewald, Fabian, Alessandri, Riccardo, Kroon, Peter C., Monticelli, Luca, Souza, Paulo C. T., Marrink, Siewert J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.01.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 119/118; 631/114/794; 631/57/2266; 639/301/1034; 639/638/455; Algorithms; Animals; Biochemistry, Molecular Biology; Biophysics; Block copolymers; Chemical Sciences; Complex systems; Computational Biology; Computer Science; Condensed Matter; Graph matching; Humanities and Social Sciences; Life Sciences; Lipids; Liquid phases; Macromolecular Substances - chemistry; Macromolecules; Material chemistry; Materials Science; Modeling and Simulation; Molecular dynamics; Molecular Dynamics Simulation; multidisciplinary; Nanomaterials; Nanostructures - chemistry; Nanotechnology; Nucleic Acid Conformation; or physical chemistry; Physics; Polymer melts; Polymers; Random walk; Science; Science (multidisciplinary); Simulation; Single-stranded DNA; Software; Theoretical and; Topology
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-27627-4

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle. To facilitate the rational design of (nano)-materials and biomacromolecules by MD simulations, the authors present the polyply suite, featuring a graph matching algorithm and a random walk protocol for generating multi-scale polymeric topologies and initial coordinates.