A Transparent, Reproducible, Usable by Others, Extensible (TRUE) simulation workflow of a graphene slit pore.
A small bug was discovered in the number density calculation which caused the averaging to be incorrect. The bug has since been fixed and the changes are reflected in the reference data. Therefore the figure generated from this notebook will slightly differ than the number density figure in the paper. However, the new number density data is not qualititatively different and does not change any of the major conclusions of the paper.
All of the files needed to build and run this simulation are contained within this workflow. Additionally, the Python functions and classes to initialize and parametrize the system are freely available on GitHub, making the workflow transparent. Because all of the files and code are freely available, any user should be able to run this simulation and get similar results, making this workflow reproducible.
Any user of this worklow is also free to change any of the system or simulation parameters. For instance, the temperature this simulation is run at can easily be changed within the GROMACS mdp files contained in this repository. Thus making the workflow usable by others and extensible.
There are several software requirements to successfully run this workflow: