units           lj
atom_style full
dimension  3
neighbor        0.5 bin
neigh_modify    every 1 delay 3 check yes
atom_modify sort 0 0
boundary p p p
read_data cylinder.dat
group sample type 2
thermo 50
thermo_style one
timestep	0.01
fix 1 sample langevin 1.0 1.0 1.0 65439
fix 2 sample nve
region 2 cylinder z 0.0 0.0 1.0 -50.0 50.0 side in units box
pair_style table linear 500
pair_coeff 1 2 tanh_potential_50.table TANH_POTENTIAL
pair_coeff 1 1 tanh_potential_50.table TANH_POTENTIAL
pair_coeff 2 2 tanh_potential_50.table TANH_POTENTIAL
pair_write 1 2 500 r 1.0 10.0 tanh_potential_50.tab TANH_POTENTIAL
pair_write 1 1 500 r 1.0 10.0 tanh_potential_50.tab TANH_POTENTIAL
pair_write 2 2 500 r 1.0 10.0 tanh_potential_50.tab TANH_POTENTIAL
fix wall all wall/region 2 lj126 1 1 2.5
compute 1 sample msd
variable msd equal c_1[4]
variable ts equal 1*step
variable xx equal xcm(sample,x)
variable yy equal xcm(sample,y)
variable zz equal xcm(sample,z)
dump   1   all   custom   100   square_well_50.dump  id  x y z  ix iy iz
dump_modify   1   format "%d %.5f %.5f %.5f %d %d %d"
fix 3 all print 1 "${ts} ${msd}"  file square_well_50.out screen no
fix 4 all print 1 "${ts} ${xx} ${yy} ${zz}" file square_well_50.xyz screen no
reset_timestep 0
run 100000