I used to build some small molecules using Avogadro. Now, I want to build a large molecule, Graphene oxide which unfortunately doesn't have a definite structure with different levels of oxidation. Can someone please suggest me how can we build such single sheet/layer of Graphene Oxide (GO) on Avogadro or any other tools? I will be extremely grateful for any inputs/suggestions.


2 Answers 2


You asked as well on the Avogadro forum, but I'll include my answer here for others:

For GO, there are two fairly commonly used Python packages:

I admit I haven't used either of them, but from what I can tell, GOPY is maybe a bit more flexible, but only generates PDB files, and MakeGraphitics will generate parameters to use in LAMMPS.

Both could be integrated into Avogadro v2 as plugins.


I think that drawing the molecular form should not be so hard, accordingly to the structure bellow.

But, you can use the supplementary data from the reference below and download, the structures they use in their calculations, the modify it as your needs.

Reference: F. Mouhat, F-X. Coudert, and M-L. Bocquetc, Structure and chemistry of graphene oxide in liquid water from first principles, Nature Communications volume 11, Article number: 1566 (2020). DOI: 10.1038/s41467-020-15381-y.
Github data repository can be downloaded here.
Full trajectory data can be donwloaded from Zenodo.

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