Why the system becomes chaotic after equilibrium?

Thank you very much for your advice.

Please always reply to the mailing list, not just individuals. Thanks.

I have tried to change the periodic boundary into S along X direction and
increase the distance between the sphere and the plate, but the results
still are not very ideal.

"Not very ideal" is a bad description and people on the mailing list
learn almost nothing from this description.

Sphere too close to the plate is just one source of error; there could
be others. For example your sphere may be too small to be stable in
vacuum, or the potential is not suitable for describing an isolated
sphere.

You also have not defined what "chaotic" mean. Was it used to
describe the sphere or the plate?

Maybe I do not know what the distance should be?

What is the length of the potential cutoff?

How to add the vacuum you said? Would you like to give me some specific
advice?

Vacuum in this context is "a space with nothing". Use the boundary
command to add space along your vacuum direction. But note this has
the same effect as changing the boundary to be non-periodic.

Ray