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Graphene Oxide sheet models (GAFF2-AIM) in GROMACS format


  • CP2K_OPT_GEO.xyz is the optimized coordinates from CP2K in XYZ format

  • DDEC6_even_tempered_net_atomic_charges.xyz and DDEC_atomic_Rcubed_moments.xyz are the Chargemol output files with atomic charges and volumes

  • GO_sheet_#_#.gro is the initial coordinates (produced with the MakeGraphitics library) in GROMACS format

  • GO_sheet_#_#.top is the GAFF2-AIM topology in GROMACS format

  • amber99sb-ildn.ff-modified/ is the amber99sb-ildn force field in GROMACS format, modified with GO sheet parameters (taken from https://www.bio2byte.be/acpype/)

Note: Since these structures are periodic in the XY plane, they are meant to be used with the "periodic-molecules = yes" option in the *.mdp file of GROMACS.

Don't forget to cite ;)


Pinto, A.V. et al. (2022) “Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules” The Journal of Physical Chemistry B. Available at: https://doi.org/10.1021/acs.jpcb.2c06037.

Additional files can be found at the following repositories:


GO_18, files from linear-scaling DFT and non-bonded parameters calculations https://zenodo.org/record/7323314#.Y7w_Q9LP1AM

GO_20, files from linear-scaling DFT and non-bonded parameters calculations https://zenodo.org/record/7323388#.Y7w_sdLP1AM

GO_22, files from linear-scaling DFT and non-bonded parameters calculations https://zenodo.org/record/7323436#.Y7w_zdLP1AM

GO_24, files from linear-scaling DFT and non-bonded parameters calculations https://zenodo.org/record/7323444#.Y7w_5tLP1AM

GO_26, files from linear-scaling DFT and non-bonded parameters calculations https://zenodo.org/record/7323454#.Y7w__dLP1AM

GO_28, files from linear-scaling DFT and non-bonded parameters calculations https://zenodo.org/record/7323465#.Y7xAJNLP1AM

GO_30, files from linear-scaling DFT and non-bonded parameters calculations https://zenodo.org/record/7323484#.Y7xAOtLP1AM


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