Hello, I have a question about molecular dynamics and I wi be appreciated if you answer me please. I have performed nvt equilibration step on a system consisting of lipid and cyclic peptide nanotube and actually it’s cell membrane embedded peptide nanotube. In some regions of the bilayer, the lipid molecules are close to each other and tangled. What can be the reason? Is something wrong with my work?

Thank you so much in advance, I really appreciate your response and help.