Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane

Simulation files are included as follows:

gro_atmd.zip

Coordinate (*.gro) files from atomistic simulations

gro_cgmd.zip

Coordinate (*.gro) files from coarse-grained simulations

Each gro_*.zip file includes (i) the initial coordinates of each simulation system, and (ii) the final coordinates of each simulation replicate of each system.

Note: Coordinates of water molecules are excluded to reduce file sizes. Nonetheless, the number of water molecules in each system is mentioned in the corresponding *.top files.

mdp_topol.zip

MD simulation parameter (*.mdp) files

Topology (*.top) files - info on the number of molecules of each component in the simulation system

itp.zip

Topology parameter (*.itp) files describing atom type, bond, angle, dihedral etc. for each protein, lipid, polymyxin and solvent type.

ATMD directory - atomistic simulations

CGMD directory - coarse-grained simulations

Numerical source data for each quantitative plot (based on figure numbers) are provided in : Num_data_for_quant_plots.zip