  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 leverages 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 melt simulations of six different polymers using two
force-fields with different resolution. We further demonstrate the power of our
approach by setting up a multi lamellar microphase-separated block copolymer
system for next generation batteries, and by generating a liquid-liquid phase
separated polyethylene oxide-dextran system inside a lipid vesicle, featuring
both branching and molecular weight distribution of the dextran component.
