Effects of Coulomb and vdW modifiers on hydrogen-bonds, energy and structural properties of peptide nanomembranes: A study by Molecular Dynamics simulations

In this study, four independent Molecular Dynamics simulations were conducted to evaluate how the calculation method of Coulomb and van der Waals (vdW) interactions (Cut-off or Particle-Mesh-Ewald - PME), and their modifiers: None, Potential-Shift (PS) or Potential-Shift-Verlet (PSV) affect the energetic and structural properties of A6H peptide nanomembranes. The results indicate that the use of cut-off as a basic method for calculating interactions may result in a more pronounced interaction, significantly affecting important characteristics of peptide nanomaterials, especially when compared with results obtained with PME/PSV. Hydrogen bond lifetime, a key feature of peptide nanomaterials, is strongly affected by the modifier used, resulting in a significant impact on self-assembled structures with a highly aligned peptide beta-sheet structure.