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

Citation (APA 7)

Grünewald, F., Alessandri, R., Kroon, P. C., Monticelli, L., Souza, P. C., & Marrink, S. J. (2022). Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials. Nature communications, 13(1), 68.

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.