atoms overlapping

I can’t visualize your data file correctly. It seems just one overlapped particle and I don’t know why.

I think it is better to build the initial configuration with another method and test it again.

As I know we shouldn’t have any overlap in the system after the minimization step (actually it is one of the minimizing’s duties to solve these kinds of issues).
And if there is any overlap in the system in the usual way, your run will stop somewhere with some famous LAMMPS errors.