Script to build the pMMO hexameric array
python hexarray.py
Then need to add the file to remove the lines END TER
Script to build a small cylidrical bilayer in pMMO pore.
The first script reads a template MDP file (template.mdp) that contains pull restraints for one pMMO, and writes a new MDP file with updated pull-group and pull-coord definitions to account for multiple copie
The second script reads a template index file that defines groups for one unit cell and writes a new index file with the same groups replicated for each pMMO copy. Each subsequent copy has its atom indices shifted by the number of atoms per unit.