as you do not provide the whole script to reproduce the problem, I'd guess that you have some really wild dynamics somewhere (physically incorrect setup of the calculation). See, even if your carbon nanotube has temperature of 0.5 K (you use metal units?), mean kinetic energy per atom, divided by Boltzmann constant (temperature) is more than four thousand degrees (other parts of a system fly around? do they interact with cnt?).
Second question - are your potential parameters consistent with "units" setting? Another related problem is that not every classical potential may work for 4500 K, and none of them is correct for 0.5 K (classical potentials are not correct below Debye temperature).
There is also a question about correctness of the temperature calculation. E.g., you do not seem to take into account center-of-mass velocity (see compute temp/com documentation for details).
06.11.2013, 15:23, "Daniel.Mulvihill" <[email protected]>: