MD Files for "First inhibitor of a bacterial two-partner secretion system" [POTRA1+2-P1; Replicate 3]

Welcome! Files pertaining to the MD simulations conducted for the "First inhibitor of a bacterial two-partner secretion system" paper are deposited here: Contents: POTRA1+2-P1 Replicate 3 (Used in Fig. 4b and S8) All simulations are conducted (n = 3). Each folder contains files used for input or output (in .zip format). Note for POTRA1+2-P1 simulations: each replicate is stored in a separate repository due to storage file-size limitations. Link to Replicate 1: DOI 10.5281/zenodo.18639446 Link to Replicate 2: DOI 10.5281/zenodo.18639780 Used for all 3 Replicates per system Initial AlphaFold2 Predicted Structure (.pdb) Cleaned Initial Structure (.pdb) Processed separately per replicate GROMACS Initial Setup Files (.gro,.itp) GROMACS Structure Configuration Files (.gro) GROMACS Solvation Setup Files (.gro,.top) GROMACS Energy Minimisation Files (.gro,.edr) GROMACS NVT Equilibration Files (.gro,.cpt) GROMACS NPT (with constraint) Equilibrium Files (.gro,.cpt) GROMACS NPT (without constraint) Equilibration Files (.gro,.cpt) GROMACS Production Structure, Trajectory, and Other Files (.gro,.pdb,.trr,.xtc,.edr,tpr) GROMACS PBC Fixed Trajectories (in the order below) -pbc -whole -ur compact tric -> -pbc -nojump -ur compact -tric -> -pbc -mol -ur compact -centre tric [Trajectory used for final analysis] And logs corresponding to each setup (.txt).