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lammps/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.min
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# -------- 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
# Read in the coordinates generated by packmol:
# (This takes a while, unfortunately.)
include system.in.coords
# If you repeat minimization later, you can skip the (slow) step above which
# reads the coordinaes, by commenting it out and uncommenting this line below:
#
# read_restart system_t0.rst
# -- Settings Section --
include system.in.settings
# -- Run section --
write_restart system_t0.rst
dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
# minimize
minimize 1.0e-5 1.0e-7 5000 20000
# If minimization crashes, then instead try Langevin dynamics
# with a small timestep and a fast damping parameter. For example:
#
# timestep 0.05
# fix fxlan all langevin 300.0 300.0 100.0 48279
# fix fxnve all nve
#
# run 10000
write_restart system_after_min.rst
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