Input files and output data for MD simulations of NCYIWM, AERSVR, and VQIVYK peptide systems

Herewith can be found the input files that have been used for the all-atom equilibrium moleculars dynamics (MD) simulations (CHARMM36m-TIP3P) conducted on the peptides NCYIWM and AERSVR from the human DPF3a protein, as well as on the VQIVYK PHF6 peptide from the human tau protein. Along with the in-house Python scripts used for data treatment or specific analysis (e.g. secondary structure), the corrected trajectories (xtc) and coordinates (gro) obtained after running the simulations (from the corresponding tpr files) for each tested system (steric zippers, free hexapeptides, and seed) are also enclosed. Associated generated data and results have been described in the following pre-print publication by Mignon J., et al. submitted as an original research article in the Journal of Chemical Information and Modeling (ACS): "Identification of amyloid regions and mechanisms from sequence-based modelling and molecular dynamics simulation: a case study of the intrinsically disordered protein DPF3".