# PREREQUISITES:
#
#     You must use moltemplate.sh to create 3 files:
#        system.data  system.in.init  system.in.settings
#     (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
#
# -------- REQUIREMENTS: ---------
# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
#   http://lammps.sandia.gov/doc/Section_start.html#start_3
# 2) It also may require additional features and bug fixes for LAMMPS.
#   So, after typing "make yes-user-misc" in to the shell, ...
#   be sure to download and copy the "additional_lammps_code" from 
#   http://moltemplate.org     (upper-left corner menu)
# 3) Unpack it
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
# 5) Compile LAMMPS.
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
#

# -- Init Section --

include system.in.init

# -- Atom Definition Section --

read_data system.data

# -- Settings Section --

include system.in.settings

# -- Run Section --

#minimize 1.0e-5 1.0e-7 500 2000

timestep      10.0  # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
dump          1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz


thermo_style  custom step temp pe etotal vol epair ebond eangle
thermo        1000  # time interval for printing out "thermo" data


fix fxlan all langevin  300.0 300.0  120 48279
fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy


# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
#        (for the "epsilon" used by the coarse-grained lipid), and
#       to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein)
# Note: The langevin damping parameter "120" corresponds to 
#       the 0.12ps damping time used in Watson et. al JCP 2011.
# Note: We maintain the system system at constant (zero) tention 
#       using a barostat damping parameter Pdamp=1000 ("0 0 1000")


# optional (not sure if this helps):
# balance x uniform y uniform


run           100000

write_data   system_after_npt.data