Hi Peter! Thanks for your response. The same thing happens with 10m steps. I would expect them to form into a random formation, where the lipids are spread within the water with their hydrophobic sides outwards. Also, if you check the energy of the system it's stable which I don't really expect this...

This is my example of how I am saving using MDAnalysis (where "mda.") Of course I am using different formats but still def write_trajectory_vid(): print('Writing trajectory to video') u = mda.Universe(formatted_folder_name + '/exit_state.pdb', formatted_folder_name + '/trajectory.dcd') with mda.Writ...

Hello peeps I might be confused but once I add Water into my system it seems that it has reached a stable state. I keep adding heat over some time but the molecules just move in their positions. I am setting the lipids in a spherical formation with two layers (inner and outer). It seems that they br...