VMD-L Mailing List

From: Nd S (navdeep79_at_gmail.com)
Date: Mon Sep 22 2008 - 15:26:20 CDT

Hi

I am working on carbon nanotubes, by putting it in a periodic box. The BC
are periodic. I am concerned that the nanotube is aligned in the z
direction, the atoms on the start of the nanotube and at the end of the
nanotube are different, but by the application of periodic BCs the atoms at
the end of nanotube in one box and the start of its periodic image virtually
share the same space. . How NAMD is going to handle this. Also there are no
bond defined between these atoms.

Thanks
Navdeep