# -- Init Section --

include system.in.init

# -- Atom Definition Section --

# I you want to be careful, you can minimize the system first.  (Try using 
# "run.in.min" and uncomment the read_restart command in this file below.)
# read_restart system_after_min.rst

read_data system.data

# -- Settings Section --

include system.in.settings

# -- Run Section --


timestep        0.025
dump            1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz

# 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.)

# Keep the chaperonin fixed.  Only let the protein move.

fix fxlan proteins langevin 0.39 0.39 1.0 48279
fix fxnve proteins nve

# Notes:
# The temperature is in reduced units and is set to 0.39
# which is the folding temperature for the unfrustrated protein.
# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
# as it was in the paper.  (Hopefully folding times should be similar.)
# (See http://lammps.sandia.gov/doc/fix_langevin.html)


thermo_style    custom step temp pe etotal press vol epair ebond eangle edihed
thermo_modify   norm no  #(report total energy not energy / num_atoms)
thermo          50     #(time interval for printing out "thermo" data)

#restart         100000000  restart_nvt

run		5000

write_restart  system_after_nvt.rst