Molecular Dynamics Simulations of Antimicrobial Peptide KU04AMP01 and Gram-Negative Membrane Bilayer

This dataset contains molecular dynamics simulation trajectories, coordinate files, and topologies for the experimental antimicrobial peptide KU04AMP01 interacting with a model Gram-negative membrane bilayer. Both all-atom (AA) and coarse-grained (CG) simulations data are present. These simulations are designed to investigate the mechanistic action of KU04AMP01, specifically focusing on multi-peptide membrane disruption, bilayer penetration, and mass density profiles. Methodological Details & System Setup: Simulation Software: GROMACS Force Field: Martini3 (Coarse-Grained - prepared by vermouth-martinize and COBY V 1.0.14), CHARMM36 (All-Atom - prepared by CHARMM-GUI V 3.7) Peptide Composition: KU04AMP01 is an Antimicrobial Peptide derived from Pseudomonas bubulae KU04, a psychrotolerant bacterium isolated from the Kupup Lake ecosystem in Northeastern India. Conformations determined by AlphaFold. FASTA sequence: DNKAKSKKRDKEKPSSGRPGQTNSVPNAAIQVYKED Membrane Composition: The Gram-negative membrane model consists of a symmetric bilayer with 46% DVPE, 25% POPE, 19% POPG, 8% DOPE, and 2% TOCL. The composition was calibrated to maintain an area per lipid of $\sim 0.61\;nm^2$ to accurately mimic biological membrane fluidity. System Architecture: The CG simulations feature both control (membrane only), single peptide-membrane, and a 12-peptide horizontal grid configuration with membrane. The AA simulations feature single peptide-membrane complexes with mutually orthogonal peptide orientations. Box Dimensions: $14 \times 14 \times 12\;nm^3$ with periodic boundary conditions. Contents: The dataset includes all critical steps of the simulation pipeline: Initial system topologies and coordinate files (.gro, .top, .itp). Trajectory data covering energy minimization, NVT/NPT equilibrations, and production runs. Source Code Availability: The automation scripts, source code, and Jupyter notebooks (e.g., gromacs_ku04amp01_membrane_martini3) used to build the system and generate this dataset can be found in the corresponding GitHub repository: hariseldon99/gromacs_sims/Antimicrobial_Peptides/Ku04AMP01_Membrane_Bilayer.