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

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.
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Contributor : Paulo Telles de Souza Connect in order to contact the contributor
Submitted on : Wednesday, November 16, 2022 - 2:12:20 PM
Last modification on : Tuesday, November 22, 2022 - 3:46:38 AM


s41467-021-27627-4 (2).pdf
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Fabian Grünewald, Riccardo Alessandri, Peter C Kroon, Luca Monticelli, Paulo C T Souza, et al.. Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials. Nature Communications, In press, 13 (1), pp.68. ⟨10.1038/s41467-021-27627-4⟩. ⟨hal-03855658⟩



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