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

Fabian Grünewald, Riccardo Alessandri, Peter C. Kroon, Luca Monticelli, Paulo C. T. Souza and Siewert J. Marrink ()
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Fabian Grünewald: University of Groningen
Riccardo Alessandri: University of Groningen
Peter C. Kroon: University of Groningen
Luca Monticelli: UMR 5086 CNRS and University of Lyon
Paulo C. T. Souza: UMR 5086 CNRS and University of Lyon
Siewert J. Marrink: University of Groningen

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-021-27627-4

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