
# Create the coordinates of the atoms using PACKMOL
cd packmol_files

  packmol < mix_lipids+water.inp
  mv -f system.xyz ../moltemplate_files/

cd ..



# Create LAMMPS input files this way:
cd moltemplate_files

  # run moltemplate

  moltemplate.sh -xyz system.xyz system.lt

  # This will generate various files with names ending in *.in* and *.data.
  # Move them to the directory where you plan to run LAMMPS (in this case "../")
  mv -f system.data system.in* ../

  # Optional: Move the "log.cite" file (containing links to relevant papers).
  mv -f log.cite* ../

  # Optional:
  # The "./output_ttree/" directory is full of temporary files generated by
  # moltemplate.  They can be useful for debugging, but are usually thrown away.
  rm -rf output_ttree/

  # Optional:
  # Delete the "system.xyz" file we created earlier with PACKMOL.
  rm -rf system.xyz

cd ../
