Thanks for replying my previous question. In my carbon nanotube, i had used periodic boundary condition along axial direction and shrink boundary condition in x & y directions.I had specified the coordinates through the input file and i had used REBO potential in NVE ensemble. But When i run the code the structure is too much deformed. I mean the atoms moved here and there in a random fashion. So, i used the command spring self to fix them to their original positions. I want to know that is it ok to use this to keep the structure intact because this may add extra force on each atom. Also, will the magnitude of spring constant i specify in this command effect the thermal properties of the structure??