Forcefields, MD trajectories and snapshot geometries for "Unravelling charging and discharging processes in organic radical-based electrodes - a hierachical molecular and quantum mechanical approach"

ffs.zip: Contains forcefields for the three different F-pentamers, tetrabutylammonium (Bu4N+), hexafluorophosphate (PF6-) and acetonitrile. A monomeric unit of the F-pentamer consists of a terthiophene to which a 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO) is attached to via a formamide-linker. The first F-pentamer has a positiviely charged TEMPO moiety (FNO.itp), the second F-pentamer is not charged (FU.itp) and the last F-pentamer has a positively charge thiophene-backbone (FT.itp). SOC100_uncharged.zip: Contains gromacs[1] trajectories (every 10th frame of the original trajectories) and TPR-files for the three production runs of the simulation cell containing 18 F-pentamers with charged TEMPO-moieties, 354 Bu4N+, 494 PF6- and 1853 acetonitrile molecules. SOC0_uncharged.zip: Contains gromacs trajectories (every 10th frame of the original trajectories) and TPR-files for the three production runs of the simulation cell containing 28 uncharged F-pentamers, 354 Bu4N+, 354 PF6- and 2253 acetonitrile molecules. SOC50_chargedNO_chargedThio.zip: Contains gromacs trajectories (every 10th frame of the original trajectories) and TPR-files for the three production runs of the simulation cell containing 14 uncharged F-pentamers, 7 F-pentamers with charged TEMPO moieties, 7 F-pentamers with charged thiophene-backbone, 354 Bu4N+, 424 PF6- and 2048 acetonitrile molecules. SOC50_chargedNO.zip: Contains gromacs trajectories (every 10th frame of the original trajectories) and TPR-files for the three production runs of the simulation cell containing 14 uncharged F-pentamers, 14 F-pentamers with charged TEMPO moieties, 354 Bu4N+, 424 PF6- and 1876 acetonitrile molecules. snapshot_geometries: Contains xyz-files of all snapshots obtained from the three production runs from SOC50_chargedNO. Open valencies caused by "cuts" were padded with H-atoms using openbabel[2] (version 2.4). [1] M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess, and E. Lindahl, “GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers,” SoftwareX, 1–2 19–25 (2015) [2] Noel M. O’Boyle, Michael Banck, Craig A. James, Chris Morley, Tim Vandermeersch, Geoffrey R. Hutchison "Open Babel: An open chemical toolbox." J. Cheminf., 3, 33 (2011).