Thank you very much, Ray!
I used fix temp/rescale to rescale the temperature of the top and bottom 2 layers of atoms of the cylinder, and fix nve, fix recenter applied to whole atoms. But in such a short time, the change of KE and PE of the PKA and particular atoms are so large. I do not know whether this is abnormal. How can I check this?
Sorry, what do you mean by “Does this occur without the PKA?”? Do you mean all the input files are same except that there is no PKA induced? I think the atoms seems outside the surface is because some atoms are sputtered out. And also maybe the thickness of the line which indicates the surface is not thick enough, that makes it feels like atoms are outside the surface.