Laminar peptide structure: Energetic and structural evaluation using molecular dynamics

Exploring How System Dimensions and Periodic Boundary Conditions Influence the Molecular Dynamics Simulation of A6H Peptide Self-Assembly Nanostructures

“…Thus, using GROMACS tools, a dimer was constructed using two A 6 H monomers, one inverted relative to the other, as shown in Figure . This dimer was then replicated 10:10 times on x- and y -axes, forming the β-sheet nanomembrane structure A 6 H (referred to here as A 6 H-11), favoring hydrogen bonds (HBs) that are crucial for maintaining β-sheet nanostructures. , This structure was then solvated in water (modeled with TIP3P − ), forming two layers of water molecules (about 3 nm each), positioned in contact with each of the membrane surfaces.…”

“…For fibers cases, the use of a short fiber may obscure interpretations of ripple and twist effects, as the fiber’s ends are confined within the same degree of freedom. This effect was demonstrated by de Andrade et al , For membranes, restricting the simulation area of the membrane creates constraints at the membrane edges that may hinder the converged analysis of a structural or energetic property. However, choosing the dimensions of the simulated structure and managing computational costs are challenging balancing acts.…”