strange behavior of thermo

Atoms losing in your simulation can be the result of anything, -bad geometry, overlapped atoms, large timestep… What i figured is that since you are using nve ensamble, and no temp. rescaling, ur system has very high p.e, which being converted to your k.e makes you loose your atoms. Try improving your geometry or reduce your timestep. You can also use thermo_modify lost warn command to have an insight as to what is happening.