Antimicrobial peptide insertion of oligomers into E.coli type membrane

The repository contains the raw simulation data supporting the all-atom molecular dynamics analysis reported in the manuscript. It is organized into five top-level directories, one per simulated system: linear (L33, KKIRVRLSA), l8 (KKIRVRLVA), dimer (DIM-33), tetra (SET-M33), and umbrella_sampling. The four peptide directories share an identical internal structure comprising four subdirectories: 00_system, containing force field files (CHARMM36m, July 2022 release), topology, index, non-standard residue parameters, and the initial peptide coordinate file; 01_protocol, containing equilibration MDP files (steps 6.0–7.2) and the production MDP file; 02_starting_point, containing the biased equilibration output used as the starting frame for production runs; and 03_production_results, containing four independent replicas each with the production trajectory, nojump-corrected trajectory, run input file, pull force and pull coordinate files, and RMSD, SASA, hydrogen bond count, and minimum peptide–image distance time series. The umbrella_sampling directory contains the WHAM-derived potential of mean force profiles, window histograms, peptide and membrane center-of-mass coordinate files, and window frame selection data for L33, L8, and DIM-33.