I have modeled a cnt through vmd with a molecular atom style(bonds,angles, dihedrals included).
I am using periodic boundary conditions and a box that is quite larger(10 times) than the dimensions of the cnt in x,y directions and equal to the dimension of cnt in z direction.
During equilibration i use an npt fix 300 300 1 iso 0 0 1 drag 1
I run it for 400000 time steps and although the potential energy equilibrates and the temperature somewhat does the box is expanding 5 times its size and does not stabilize.
I also get a warning : bond/angle/dihedral extent >half of periodic box size.
If you any idea about the cause of the problem or any suggestion regarding its fix please let me know.
Thank you very much,