# Here we generate the starting coordinates of the simulation
# using PACKMOL

# You must run each packmol commend one after the other
# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding
# "inp" file. This should not happen. You can also usually interrupt
# packmol after 30 minutes, and the solution at that point should be good
# enough for use.
packmol < step1_proteins.inp # This step determines the protein's location
# It takes ~20 minutes (on an intel i7)
packmol < step2_innerlayer.inp # this step builds the inner monolayer
# It takes ~90 minutes
packmol < step3_outerlayer.inp # this step builds the outer monolayer
# It takes ~4 hours

# Running these three commands will probably take about an hour.
# (It depends on how uniformly you need the packing to be.)

mv -f step3_outerlayer.xyz ../system.xyz