Fig. 1: Schematic illustration of the workflow for parameter file generation.
From: Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials
Polyethylene oxide (PEO) grafted methyl acrylate (MA) is used as an illustrative example. The user input is the residue graph, while the building blocks are taken from the library (presented in dashed boxes). However, users can modify the library as they need. In step one, the parameters for the blocks are applied based on the residue graph to form a disconnected graph at the target resolution. In step two the links are matched at residue graph level to the input residue graph. Subsequently, links are applied to the disconnected graph at target resolution in the third step producing the complete parameter file.
