Molecular Dynamics Simulation Dataset: POPC Bilayers at Varying Sizes (256, 512 and 1024 lipids) and Hydrations (40, 80 and 160 water/lipid) Analyzed with CPPTRAJ, GROMACS, MDAnalysis, and LiPyphilic

This dataset contains 500 ns all-atom Molecular Dynamics (MD) trajectories and analysis scripts for POPC bilayers, covering system sizes of 256, 512, and 1024 lipids at hydration levels of 40, 80, and 160 waters per lipid. The data supports a two-fold study: Biophysical Convergence: Assessing how structural properties (APL, thickness) and dynamic properties (order parameters, headgroup tilt, diffusion) converge as a function of membrane size and hydration. Software Benchmarking: Comparing the accuracy and computational performance of four major analysis packages: CPPTRAJ, GROMACS, MDAnalysis, and LiPyphilic. Repository Contents To reproduce the trajectory analysis Raw (continuous/unwrapped) and pre-processed (centered/imaged) trajectory files sampled at 1 ns/frame, topologies and index files (folder trajectories_topology_indices.zip). A complete set of Bash and Python scripts used to calculate Area Per Lipid (APL), Bilayer Thickness, SCD Order Parameters, Headgroup Orientation, and Lateral Diffusion (MSD), and software benchmark (folder scripts). Refer to the readme.md file for guidance. To reproduce the Simulations Simulation topologies and index files required to reproduce the simulations (folder MD_simulations_input&topology_files.zip). Refer to the readme.md for for guidance.