Supplementary Code and Data

This repository includes data and code from the Accurate large scale modelling of GrapheneOxide: ion trapping and chaotropic potential at the interface paper. It gives a breakdown of using the makegraphitics code ¹ for making the graphene-oxide sheet structure and forcefield.

Graphene Oxide Builder

MakeGraphitics is a library to ceate atomistic graphene oxide structures for molecular dynamics.

Output:

• .xyz
• lammps data file

Automatically parameterise by OPLS forcefield.

Install

Clone this repository. Install using Python2.7. Run the tests to check the installation has worked.

git clone https://github.com/velocirobbie/make-graphitics
cd make-graphitics
python setup.py install
pytest

A conda environment is provided if you do not have the right packages. If you have conda set up, execute these commands to create a working python environment before the install setp.

conda env create --file graphene-env.yml
conda activate graphene

Instructions

Make a rectangular graphene sheet that extends through periodic boundaries. Parameterised with OPLS and outputs to .xyz for easy veiwing with VMD and a LAMMPS data file.

python2.7 GO_rect.py

There are several tunable parameters in GO_rect.py that you may be interested in. Including:

• sheet dimensions
• C/O target ratio, ratio
• Rate at which new nodes are added, new_island_freq
• output snapshots of the oxidation process every N steps with video_xyz=N. Viewed in VMD with topo readvarxyz out.xyz

DDEC parametrisation

DFT calculations of the above .xyz output can be performed using the ONETEP electronic structure calculation package. The ONETEP code version 6 is available from www.onetep.org. Instructions for implementing Density Derived Electrostatic and Chemical (DDEC) electron density partitioning are available here.

The Lennard-Jones parameters can be calculated using the Tkatchenko-Scheffler relations using the QUBEKit package. Installation and instructions are available here. The charge and Lennard-Jones parameters from QUBEKit are exported into a Gromacs .itp using the pre-existing OPLS .itp forcefield file.

Data conversion

Output LAMMPS .data files were converted to Gromacs .itp format using in-house code. Other data conversions, such as structure files (.xyz to .gro) can be converted using MDAnalysis and/or built-in Gromacs tools.

Supplementary Data

The OPLS and DDEC forcefield files for the GO sheet used in this paper is provided in the example_input folder.

Citing

¹: The work contained here has been published in the following papers:

• Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold https://doi.org/10.1021/acs.jcim.9b00114

• Accurate large scale modelling of Graphene Oxide: ion trapping and chaotropic potential at the interface (in preparation)

@article{albadri2020accurate,
  title={Accurate large scale modelling of GrapheneOxide:  ion trapping and chaotropic potential atthe interface},
  author={al-Badri, Mohamed Ali and Smith, Paul and Sinclair, Robert C and al-Jamal, Khuloud and Lorenz, Christian D},
  journal = {Carbon},
  volume = {},
  number = {},
  pages = {},
  year = {2020},
  doi = {},
}
@misc{albadri2020accurate-github,
    url = {https://github.com/maalbadri/Accurate-large-scale-modelling-of-GrapheneOxide},
    howpublished = {\url{https://github.com/maalbadri/Accurate-large-scale-modelling-of-GrapheneOxide}},
    note = {Accessed: \today},
    author = {al-Badri, Mohamed Ali and Sinclair, Robert C.},
    year = {2020}
}
@article{sinclair2019modelling,
  title={Modelling nanostructure in graphene oxide: inhomogeneity and the percolation threshold},
  author={Sinclair, Robert Callum and Coveney, Peter Vivian},
  journal = {Journal of Chemical Information and Modeling},
  volume = {59},
  number = {6},
  pages = {2741-2745},
  year = {2019},
  doi = {10.1021/acs.jcim.9b00114},
}
@misc{make-graphitics-github,
    url = {https://github.com/velocirobbie/make-graphitics},
    howpublished = {\url{https://github.com/velocirobbie/make-graphitics}},
    note = {Accessed: \today},
    author = {Sinclair, Robert C.},
    year = {2019}
}