This dataset contains Molecular Dynamics trajectories of 9 endecapeptides, positioned in the pore construct. One trajectory is done in absence of any transolcating peptide. .xtc files correspond to the trajectories and the .gro files contain the corresponding structures, they can be viewed, for example, with VMD. Every trajectory is the concatenation of 8 trajectories, of 125 ns each, which differ for the orientation of the centrai side-chain with respect to the frame of the pore. The following name parts indicate the central residue. The 73-80 files correspond to the construct alone, taken as a reference. 1-8 trp; 9-16 tyr; 17-24 arg; 25-32 his; 33-40 glu; 41-48 gln; 49-56 ser; 57-64 ile; 65-72 gly; 73-80 no peptide.