README.sh
5be330aa8f9flammps-icms

README.sh
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			# Here we generate the starting coordinates of the simulation
			# using PACKMOL

			# Running these three commands will probably take hours or even days.
			# (It depends on how dense and how uniformly you need the packing to be.)
			# 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

			# This should create a file named "system.xyz" (which moltemplate will read).