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

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.

The Martini Model in Materials Science

“…The fine degree of coarse-graining of the Martini model means that there is no limitation to the topology of the polymer. Recently, a tool for easily generating topologies, single chain starting structures, and morphologies of polymers has been developed by Grünewald and co-workers-Polyply [56,57]. Polyply's internal library already contains several Martini polymer models from the literature but more models can be contributed via GitHub [56].…”

“…Recently, a tool for easily generating topologies, single chain starting structures, and morphologies of polymers has been developed by Grünewald and co-workers-Polyply [56,57]. Polyply's internal library already contains several Martini polymer models from the literature but more models can be contributed via GitHub [56]. This tool standardizes and greatly simplifies the generation and setup of Martini polymer systems, as discussed more extensively in the Outlook section.…”

“…In this context, recently Grünewald and co-workers developed Polyply, a software suite for facilitating atomistic and CG polymer simulations. The tool can generate topologies of polymer systems ranging from simple or complex homopolymers, over branched and hyper-branched polymers, to block copolymers [56]. Not only single chain starting structure but also melts and more complex pre-assembled morphologies can be generated.…”

“…While properly mixing such a melt from initially disentangled chains is an almost impossible undertaking, Polyply generates such structures within minutes. Polyply's internal library already contains several Martini polymer models from the literature but more models can be contributed via GitHub [56]. This tool is expected to standardize and greatly simplify the generation and setup of Martini polymer systems.…”

“…Many Martini models are available at http://cgmartini.nl: besides an extensive number of biomolecules, and in particular lipids, a growing "polymerdome", and upcoming extensive Martini 3 solvent [259] and small-molecule [273] databases will be important for materials science applications. Moreover, both the upcoming Martinize 2 [269] and Polyply [56,57] tools rely on the Vermouth library [269], which offers a consistent way of defining building blocks and keeping track of model versions, thereby contributing to better FIG. 14.…”