This dataset contains the initial atomic configurations (initial_geometry.xyz) used in ab initio molecular dynamics (AIMD) umbrella sampling simulations of alkali metal ion transport through porphyrin-based two-dimensional (2D) membranes. The simulations aim to capture free energy profiles of ion translocation processes across the membrane for four ions: Li⁺, Na⁺, K⁺, and Mg²⁺. The dataset is organized by ion type, with each subdirectory corresponding to a specific simulation window. Each window is labeled as: [WindowID]_[ForceConstant],where: WindowID (e.g., 1A, 02A, 175A, etc.) indicates a relative ion–pore distance, used to define the collective variable in umbrella sampling. ForceConstant (e.g., 50, 300, 2000) is the umbrella force constant in units of kcal mol⁻¹ Å⁻² applied in that window. Each folder contains a single file: initial_geometry.xyz — the atomic configuration used to initialize the simulation for that window. The Magnesium directory also includes a set of deprotonated membrane configurations, labeled as deprotonated_[WindowID]_[ForceConstant], used to compare the effect of deprotonation on Mg²⁺ transport.