# NOTE: YOU MUST COMPLETE STEP 1 BEFORE RUNNING PACKMOL ON THIS FILE

# Step 2: Pack the lipids in the inner monolayer around the proteins from step1.
#
# ----- Run using: -----
# packmol < step2_innerlayer.inp
#    (This takes about 90 minutes on an Intel i7 processor)


# ----- Settings:  -----

# All the atoms from diferent molecules will be at least 5.5 Angstrons apart
tolerance 5.5
# (Setting "discale" to 1.4 increases the typical separation 
#  distance to approximately 1.4*5.5 = 7.7 Angstroms.)
discale 1.4
# The other parameters below are optional:
nloop 10000
maxit 20
seed 12345
sidemax 3000.0
# What fraction of the molecules are moved during "large moves"? (default 0.05)
movefrac 0.05


# The output file name

output step2_innerlayer.xyz

# File types are in xyz format

filetype xyz


# The proteins whose position we determined earlier in step 1
# will be frozen in place during this step.

structure step1_proteins.xyz
  number 1 
  fixed 0. 0. 0. 0. 0. 0.
end structure


# 9500 DPPC lipids will be put in a shell with their hydrophilic heads
# (atom 1) pointing inwards, and their tails (atom 5) pointing outwards.


structure DPPC.xyz
  number 9500
  atoms 1
    inside sphere 0. 0. 0. 270.0
  end atoms
  atoms 5
    outside sphere 0. 0. 0. 295.0
  end atoms
end structure 

# 9500 DLPC lipids will be put in a shell with their hydrophilic heads
# (atom 1) pointing inwards, and their tails (atom 4) pointing outwards.

structure DLPC.xyz
  number 9500
  atoms 1
    inside sphere 0. 0. 0. 273.0 
  end atoms
  atoms 4
    outside sphere 0. 0. 0. 295.0
  end atoms
end structure 

