Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments

Dataset Description This dataset corresponds to the paper: "Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Envirionments." The dataset contains simulation input files, trajectories, analysis scripts, and structural files used in the study. Directory Structure and Contents 1. itps Topology (.itp) files for the following lipids: DAT PAT PDIM MYCO SGL TDM TMM 2. mapping_aa2cg Atomistic-to-coarse-grained mapping files for the lipids listed above. Atomistic coordinates are not included. For atomistic structural information, refer to the paper: "Dynamic Architecture of Mycobacterial Outer Membranes Revealed by All-Atom Simulation" by T.P. Brown 3. gromacs_scripts Scripts used for: Equilibration and production run Mean Squared Displacement (MSD) analysis Solvent Accessible Surface Area (SASA) calculations Van der Waals radii used for CG and AA SASA calculations are included. 4. python_scripts Custom Python scripts used to calculate: Pseudo-order parameter Z-dependent pseudo-order parameter PDIM-PDIM contacts Membrane heterogenity analysis 5. lipid_structures Coarse-grained coordinate files (single molecule) for each lipid listed above. 6. mdps GROMACS .mdp parameter files for Equilibration Production run 7. initial_coordinates Initial coordinates files for each simulation system described in the paper. 8. Trajectory Files (traj_*) Each trajectory archive includes: Initial coordinates Final coordinates (with velocity information, if available) Trajectory files for one simulation replica (1ns/frame, except asym_1X -> 0.1ns/frame .tpr file .top file Simulated Systems Includes A. Asymmetric Membrane (313 K) 1X 4X 16X (no final coordinate; simulation stopped before 10 us) B. Symmetric Inner Leaflet Larger Smaller Temperatures: 313, 323, 333, 338, 343, 353. At 338 K (both) and 343 K (smaller only) two trajectories are included (disordered and ordered phase) C. Symmetric Outer Leaflet (313 K) D. PDIM in Different Lipid Environments PDIM in Outer Symmetric Membrane (313 K) No final coordinate (simulation stopped before 10 us) PDIM in Asymmetric Membrane (313 K) PDIM in POPC (252, 313, 353 K) PDIM in PEPC (252, 313, 353 K) PDIM in PSPC (252, 313, 353 K) PDIM in MA (252, 313, 353 K) E. POPC only (313 K)