The voltage-dependent anion channel (VDAC) is a beta-barrel membrane protein of the mitochondrial outer membrane (MOM), which controls the transport of ions and ATP between mitochondria and the cytoplasm. The present dataset includes all data and scripts generated in the study "The intrinsically-disordered N-terminus of the voltage-dependent anion channel" by J. Preto and I. Krimm, where we performed all-atom simulations to investigate the disordered properties of VDAC’s N-terminus (i) as a free peptide in solution (ii) as part of the channel (mVDAC1-WT) or (iii) as part of a mVDAC1 mutant (mVDAC1-Cys) characterized by a disulfide bond affixing the N-terminus against the beta-barrel wall. The last two studies involve the channel embedded in a DOPC/DOPE lipid bilayer representing the MOM. Our data comprise molecular dynamics (MD) and accelerated MD (aMD) trajectories of the three systems performed for exploratory purposes. In the case of mVDAC1-Cys, MD/aMD simulations were performed upon different transmembrane (TM) potential values (0mV, +40mV and -40mV). At all voltages, GCMC/BD calculations were run to probe for possible low-conducting conformers of the channel. At +40mV, our aMD trajectory shows detachment of the N-terminus from the beta-barrel and the emergence of long-lived subconducting conformations. The stability of these conformations is further confirmed from standard MD simulations at +40mV, starting from each of the subconducting conformers identified in GCMC/BD. For each trajectory, the numbers of cations and anions crossing the channel were recorded to keep track of the intensity and of the conductance of each state.