Molecular Dynamics simulations (filtered small system)

Molecular Dynamics of E. coli ribosomes stalled by the nascent peptide SecM(Ms). Four systems were simulated: Control, K, N and WT. To facilitate analysis, each system was filtered to include all the residues within 15 Angstroms of the nascent chain, including the nascent chain, and the complete tRNA. The resulting structure is shared as a pdb file with suffix "within15_tunnel.pdb" For each system, 5x50 ns trajectories were simulated. And the concatenated trajectory is shared (suffix: "within15_concatenated.xtc")