README.sh
12150ffa7397lammm-devel

README.sh
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			# 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 (an .xyz file)
			# 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


			# NOTE: PLEASE USE "packmol", NOT "ppackmol". ("ppackmol" is the
			# parallel-version of packmol using OpemMP. This example has NOT been
			# tested with "ppackmol". Our impression was that the "ppackmol"
			# version is more likely to get stuck in an infinite loop. -Andrew 2015-8)


			# Step3 creates a file named "step3_outerlayer.xyz" containing the coordinates
			# in all the atoms of all the molecules. Later we will run moltemplate.sh
			# using the "-xyz ../system.xyz" command line argument. That will instruct
			# moltemplate to look for a file named "system.xyz" in the parent directory.
			# So I rename the "step3_outerlayer.xyz" file to "system.xyz", and move it
			# to this directory so that later moltemplate.sh can find it.

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