The present dataset holds all the input files linked to the related work, concerning the effect of the removal and displacement of membrane-bound divalent ions in models of the outer membrane of Gram-negative bacteria. This dataset presents a comprehensive collection of input data for Molecular Dynamics (MD) simulations performed using the GROMACS simulation software concerning the effect of the removal and displacement of membrane-bound divalent ions in models of the outer membrane of Gram-negative bacteria. The dataset consists of the input files stored in five tarballs each related to a part of this work: all_atom_global_stress.tar.gz: Set of simulations used to investigate the effect of divalent ions (calcium ions) removal on the properties of the outer membrane of Gram-negative bacteria. The simulations involve a set of four models of the outer membrane of Salmonella enterica, two of which are polymyxin-sensitive (P2 and P1), while the two other are polymyxin-resistant (PEtn and Ara-4N). Four replicas were made for each simulation of divalent ion removal. all_atom_local_stress.tar.gz: Set of simulations introducing a new collective variable (CV) used to study the effect of divalent ions displacement. Simulations are made for the four model membranes described in 1. For each system, a steered MD (SMD) simulation is present, where the system is pulled along the CV to create a defect in the membrane. This SMD simulation is used to calculate a free profile along the CV using an umbrella sampling (US) procedure. One simulation set is devoted to the case of the presence of a polymyxin molecule in the vicinity of the defect. coarse_grained_local_stress.tar.gz: Analog dataset as in 2. but ported for coarsed-grained MD simulations. polymyxin_e.tar.gz: Topology parameters for polymyxin E for CHARMM36 and Martini 2.2. force_fields.tar.gz: The versions of CHARMM36 and Martini 2.2 used for this work. For each membrane type, the dataset provides three replicas. The dataset includes initial and final structures (.gro files), simulation parameter files (.mdp), index files (.ndx), and topology files (.itp and .top) applicable to all systems. Refer to the manuscript and to the provided README for more information. In case of further questions, you can address them to: timothee.rivel@ceitec.muni.czVersion log: Version 1.0: initial release of the dataset Version 1.1: files in all_atom_global_stress updated for the global stress run