# test_cell2

units          real
atom_style     full
# boundary       s s s
boundary       p p p

# pair_style     lj/charmm/coul/charmm 8.0 12.0
# pair_style     lj/cut/coul/cut 8.0 12.0

pair_style     lj/charmm/coul/long 8.0 12.0
# pair_style     lj/cut/coul/long 8.0 12.0
# kspace_style   ewald/disp 0.0001
kspace_style   pppm 0.0001

dielectric     1.0
special_bonds  lj 0.000000 0.000000 1.000000 coul 0.000000 0.000000 1.000000
bond_style     harmonic
angle_style    harmonic
dihedral_style charmm
improper_style harmonic
# neighbor       2.0 nsq

read_data      test_cell2.data
# read_data      aspirin_1x1x1_opt.data 
replicate 6 6 6

# perform optimisation
# note that you do not nessesarily need to perform a dump during the minimisation step
# so it is possibly to minimise the system and then perform MD. 
# read_data      test_cell2.data
group          mobile union all
# dump           1 all atom 100 test_cell2.dump
# dump_modify    1 scale yes image yes
# # dump           2 all custom 100 test_cell2.frcdump fx fy fz
thermo_style   custom etotal
thermo_modify  line multi
thermo         100
thermo_modify  flush yes
min_style      cg
minimize       0.0001 0.000001 500 5000


# write_restart  test_cell2.rst

# Note that in LAMMPS to calcualte the energy of the system without any iteration. i.e. single point 
# run 0

# read_data      test_cell2.data
# read_dump      test_cell2.dump 1 x y z ix iy iz replace yes  

# If you performed minimisiation reset the timestep to zero
# and perform equilibration run 

reset_timestep 0

timestep       1
fix            1 mobile nve
# fix            1 mobile nvt temp 298.15 298.15 10.0
# fix            1 mobile temp/berendsen 298.15 298.15 10.0
# fix            1 mobile npt temp 298.15 298.15 10.0 aniso 1.000000 1.000000 350.0
velocity       mobile create 298.15 1415810067 mom yes rot yes dist gaussian
# dump           1 all atom 5 test_cell2.dump
# dump           1 all atom 100 test_cell2_equil.lammpstrj
# if you set 1 'scale no' it turns off the unit cell translations 
# dump_modify    1 scale yes image yes
# dump           2 all custom 5 test_cell2.veldump vx vy vz
thermo_style   custom etotal ke pe ebond eangle edihed eimp evdwl ecoul elong temp
thermo_modify  line multi
thermo         100
thermo_modify  flush yes
# restart        1000 test_cell2_1.rst test_cell2_2.rst
run            1000
# write_restart  test_cell2.rst

# do the production run 
reset_timestep 0
dump           2 all atom 10 test_cell2_prod.lammpstrj
dump_modify    2 scale yes image yes
run            1000