Simulation Input Data for "Molecular simulation of lignin-related aromatic compound permeation through Gram-negative bacterial outer membranes"

This is the reduced data behind an upcoming manuscript investigating permeability across the outer membranes of Gram-negative bacteria. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was:

tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane

Within the OuterMembrane directory, there are 3 primary subdirectories.

Build contains the scripts and files to build the simulation systems, including the CHARMM-GUI output

Equilibrium contains the equilibrium simulation inputs and the analysis scripts (subdirectory Analysis)

REUS2, which has the replica exchange inputs and essential output. It also contains an Analysis subdirectory that carries out the analysis within the text.