GOPY: A tool for building 2D graphene-based computational models
Sebastian Muraru, Jorge S. Burns, Mariana Ioniţă
Abstract
GOPY is a free and open-source Python tool specifically written to automate the generation of 2D graphene-based molecular models such as pristine graphene (PG) and several graphene derivatives i.e. graphene oxide (GO), reduced graphene oxide (rGO), aminated polyethylene glycol functionalised reduced graphene oxide (rGO-PEG-NH2), and N-doped graphene (NG) in the Protein Data Bank file format (PDB). These models are generally built manually, but the process can become lengthy and cumbersome. That is especially the case when investigating larger molecules such as those used in Molecular Dynamics (MD) simulations. Using GOPY significantly speeds up the process from hours to minutes, reducing potential bias that may come with the manual placement of functional groups on a graphene layer. Moreover, the building procedure becomes effortless for the researcher, granting the possibility of producing larger and more complex molecular models than one would be able to build manually. Of its more intensive tasks, the generation of a 4 x 4 nm2 rGO-PEG-NH2 layer takes about 9 min on a CodeOcean capsule. Each model is generated in the PDB format, which is easily convertible to a wide array of other molecular formats.