During the molecular dynamics simulation, the backbone root
mean square deviation (RMSD), which referenced the initial structure,
varied more at the beginning of the dynamics simulation and
just after reaching the equilibrium state. This result indicates that
few structural changes occurred (Fig. 9).However, structural variations
still occurred throughout the course of the simulation. These
variations are characteristic of small peptides, which are very flexible
and have various minimum energy states, indicating that these
peptides can assume different conformations (Holtje et al., 2003).
This structural modification, in turn, is related to the short amino
acid sequence, which tends to have a greater degree of freedom
(Agudelo and Patarroyo, 2010).