Molecular dynamics simulations dataset published in F. Munder et al., "A Protein Antibiotic Inhibits the BAM Complex to Kill Without Cell Entry", Nat. Commun. (2026). The dataset is organised into 4 folders: "pre_inhibited_with_pyocin", "pre_inhibited_no_pyocin", "fully_inhibited_with_pyocin", "fully_inhibited_no_pyocin", each representing the respective simulation setup listed in Table S4 of the Supplementary Information. Each folder is organised into the subfolders: "input" - contains the initial .psf and .pdb files "3_NAMD_min" - files for minimisation in NAMD "4_GROMACS" - GROMACS md simulation configuration files, prepared according to the protocol outlined in the "Methods" section of the preprint. Configuration files are only deposited for the "pre-inhibited" setups, as for the "fully_inhibited" systems these configuration files are identical. The last snapshot of replica 1 is deposited in the "4_GROMACS/2_md_simulation/1_replica1/6_prod_run/" subfolder of each simulation setup. If you use any of the simulation files from this dataset, please cite: F. Munder et al., Molecular dynamics simulations dataset published in "A Protein Antibiotic Inhibits the BAM Complex to Kill Without Cell Entry", Nat. Commun. (2026)