cGENIE user-config files used in Zhang et al. (Science Advances, 2025): "Enhanced marine biological pump as a trigger for the onset of the late Paleozoic ice age". The code for the version of the ‘muffin’ release of the cGENIE Earth system model used in this paper, is tagged as v0.9.62, and is assigned a DOI: https://zenodo.org/records/15073802. Configuration files for the specific experiments presented in the paper can be found in the directory: genie-userconfigs/PUBS/submitted/Zhang_et_al.PNAS.2023. Details of the experiments, plus the command line needed to run each one, are given in the README.txt file in that directory. This Zenodo deposit is just a copy of the above-mentioned directory 'Zhang_et_al.PNAS.2023', created upon journal request. This is definitely not the recommended way of accessing these files.