# Running LAMMPS on this file (eg. "lmp_mpi -i run.in.nvt") simulates a
# vesicle at constant NVT conditions.
#
# THIS SIMULATION WAS RUN AT HIGH TEMPERATURE (345K) IN ORDER
# TO ENCOURAGE THE LIPIDS TO FORM A SMOOTH SPHERICAL VESICLE.
# (At 300K, the lipids used in this particular coarse-grained model tend to be
#  stuck in a "gel"-like phase when arranged in a small vesicle shape, leading
#  to lumps and discontinuities.  We raised the temperature to avoid this.)
#
# -------- PREREQUISITES: ---------
# 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.
# 6) Build the system using PACKMOL and MOLTEMPLATE
#    (Follow the instructions in README_setup.sh, or run that file as a script.)
# 7) Minimize the system using:
#      lmp_mpi -i run.in.npt
#    (assuming "lmp_mpi" is the name of the lammps binary you created in step 5)
# 8) Distribute the lipids uniformly on the spherical surface using:
#      lmp_mpi -i run.in.make_uniform
#    (Why? The software tool (PACKMOL) that we used to create the initial
#     geometry for this example often leaves gaps in the packing of spherical
#     surfaces.  The "make_uniform" step should help close these holes.)
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
#
# ------------------------------- Initialization Section --------------------

include         system.in.init

# ------------------------------- Atom Definition Section -------------------

# Commenting out:
#
# read_data       system.data
#
# Instead read the data file created by "run.in.min".

# Commenting out these old commands:
#
# read_data    system.data
# read_data    system_after_min.data
#
# Instead, read the coordinates from the uniform simulation:

read_data    system_uniform.data


# ------------------------------- Settings Section --------------------------

include         system.in.settings

# ------------------------------- Run Section -------------------------------

timestep    1.0  # (the mass of each particle must be chosen accordingly)
dump        1 all custom 500000 traj_T=345K.lammpstrj id mol type x y z ix iy iz


thermo_style  custom step temp pe etotal vol epair ebond eangle
thermo        100  # time interval for printing out "thermo" data
thermo_modify norm yes flush yes


# distribute particles evenly on available processors:
fix fxbal all balance 100000 1.05 shift xyz 20 1.05

# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
# (Note: We are using "units lj", which means temperature is specified
#  in units of energy.  kB*Temp = 0.001987207*345 kCal/mole = 0.685586415)
fix fxlan all langevin 0.685586415 0.685586415 40000 48279
fix fxnve all nve

run           5000000   # (This might not be long enough for equilibration.)

write_data system_T=345K.data