##coarse-grained system run file parameters

variable temperature equal 300
variable iofrq       equal 5000
variable timesteps   equal 500000
variable dt          equal 10
variable output      string "cg_slab_eq.lammpstrj"
variable lastframe   string "cg_slab_eq.lmp"

units real
boundary p p p
molecule twomols caff.txt w.txt offset 7 0 0 0 0
atom_style template twomols

pair_style  lj/cut 11.0 #hbond/dreiding/lj/angleoffset 4 9.0 11.0  135.0 158.0
pair_modify shift yes
bond_style harmonic
improper_style harmonic

read_data cg_slab_start2.lmpdata
include monohydrate.params

#group caf_atoms type 1:7
#group wat_atoms type 8
neighbor 2.0 bin
neigh_modify delay 0 every 10 check yes exclude molecule/intra all #caf_atoms

#minimize 1.0e-4 1.0e-6 1000 100000

#velocity all create ${temperature} 34672
#variable temp_damp equal 100.0*${dt}
#variable press_damp equal 1000.0*${dt}

#fix caf_hold caf_atoms spring/self 100.0
#fix rigidify all setforce 0.0 0.0 0.0
minimize 1.0e-4 1.0e-6 1000 100000
#fix 4 wat_atoms viscous 0.1
#timestep 1
#run 2000
#unfix rigidify
#fix 4 caf_atoms rigid/small/nve molecule 
#timestep 0.1
#run       10000
#reset_timestep 0

#fix 1 caf_atoms rigid/nve/small molecule
#fix 2 wat_atoms nve

# Apply damping to relax system energy
#fix 3 all langevin ${temperature} 0.0 ${temp_damp} 12345

#timestep 0.1
#thermo 100
#run 10000

#unfix 3

#fix 1 caf_atoms rigid/nvt/small molecule temp ${temperature} ${temperature} ${temp_damp}
#fix 2 wat_atoms npt temp ${temperature} ${temperature} ${temp_damp} aniso 1.0 1.0 ${press_damp} dilate all
#timestep ${dt}

#thermo_style custom step pe ke etotal temp press density econserve
#thermo ${iofrq} 
#thermo_modify flush yes

#dump        1 all custom ${iofrq} ${output} id mol type x y z vx vy vz fx fy fz
#dump_modify 1 sort id
#run         ${timesteps}
#write_data ${lastframe} nocoeff