mbuild-cg-example.py

from numpy import pi
import mbuild as mb

cer2 = mb.load('cer2.pdb')
grid = mb.pattern.Grid2DPattern(50, 50)
leaflet, system = mb.Compound(), mb.Compound()
repeat_spacing = 6  # repeat spacing in nm
leaflet = grid.apply(cer2)  # put lipids on gird points
leaflet = mb.Compound(leaflet)
for layer_num in range(4):  # add 4 leaflets to the system
    new_layer = mb.clone(leaflet)
    if layer_num % 2 == 1:  # rotate every other layer 180deg
        new_layer.spin(pi, around=[1, 0, 0])
    new_layer.translate([0, 0, layer_num * repeat_spacing / 2])
    system.add(new_layer)
system.save('cer2.hoomdxml')