units lj
dimension 3
boundary f f p

pair_style lj/cut 1.1225
read_data thylakoid.data

pair_coeff * * 1.0 1.0
pair_modify shift yes

# Makes about 100 particles type 2:
region make_two sphere -29 0 0 6.25
region everywhere block -25 25 -25 25 -25 25
group two region make_two
set group two type 2

# And deletes some of type 1 to allow more movement:
group one type 1
set group one type 1
delete_atoms porosity everywhere 0.2 123


# Start run
variable wB equal 5.0
variable LB equal 10.0
variable lB equal 3.0
fix step all nve/manifold/rattle 1e-4 10 thylakoid ${wB} ${LB} ${lB}

thermo_style custom time step pe ke etotal temp
thermo 2500
dump traj all custom 10000 thylakoid.dump id type x y z
run 25000000