期刊
NATURE COMMUNICATIONS
卷 13, 期 1, 页码 -出版社
NATURE PORTFOLIO
DOI: 10.1038/s41467-021-27627-4
关键词
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资金
- Center for Information Technology of the University of Groningen
- ERC [669723]
- Dutch National Supercomputing Facilities through NOW
- French National Supercomputing Center CINES via GENCI [A0060710138]
- European Research Council (ERC) [669723] Funding Source: European Research Council (ERC)
Molecular dynamics simulations are crucial for material design and biomacromolecule studies. However, generating input files and starting coordinates is a major bottleneck, especially for complex systems. To address this issue, we introduce the polyply software suite, which includes a multi-scale graph matching algorithm and a generic multi-scale random walk protocol. We evaluate the quality and performance of this approach through practical applications.
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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