- Last Updated: Monday, 10 January 2022 14:02
Generating input files and realistic starting coordinates for complex multi-component simulations is often a major bottleneck, especially for high throughput protocols. 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 demonstrate the power of polyply by setting up a number of complex systems, including a liquid-liquid phase separated polymer system inside a lipid vesicle. For details, see Grünewald et al., Nature Commun. 2022.