# Equilibrate the ensemble (NVT)


# Initialization
units			real
atom_style		full
boundary        p p p

# Atom Definition
pair_style      lj/cut/coul/long 12
pair_modify     tail yes
pair_modify 	mix arithmetic
special_bonds 	lj 0.000000 0.000000 0.500000
special_bonds 	coul 0.000000 0.000000 0.833300
bond_style 		harmonic
angle_style 	harmonic
#dihedral_style 	charmm
#improper_style 	cvff


read_restart		B-npt.restart



# Settings
neighbor        2.0 bin
neigh_modify    delay 0 every 1 check yes
timestep        1
kspace_style 	pppm 0.00001

# GROUPINGS (Select all that apply)
#fix spce if have water in system, hbond for other systems
fix spce all shake 0.0001 20 0 m 1.0 a 1
#fix hbond all shake 0.0001 20 0 m 1.0

# Running and Output

# rescale simulation box during simulation
# taken from last 1 ns of npt run time, the average is 1.19982, the density of the  
# restart file above (as seen from npt.log.lammps) is 1.1865927 
variable vscale equal "(1.1865927/1.19982)^(1/3)"
fix RESCALE all deform 1 x scale ${vscale} y scale ${vscale} z scale ${vscale}

fix 1 all nvt temp 300.0 300.0 1000.0
variable dens equal "1.660538863*(mass(all) / vol)"

thermo_style    custom step temp epair emol pe ke etotal press vol enthalpy v_dens
run				10000 # 10ps of runtime in at constant temperature scaling the box
unfix			1
unfix			RESCALE

thermo			100
dump			12 all custom 50 dump.nve-pro.xyz id mol type x y z xu yu zu
dump_modify		12 sort id
restart			100 A-nvt.restart B-nvt.restart


fix 1 all nvt temp 300.0 300.0 100.0
variable dens equal "1.660538863*(mass(all) / vol)"
thermo_style    custom step temp epair emol pe ke etotal press vol enthalpy v_dens
run				1000000 # 1ns of runtime in at constant temperature
unfix			1