CNT modeling

From: Jonathan Lee (
Date: Tue Jun 12 2007 - 15:29:49 CDT

Hello all,
  I am a new NAMD user. I am trying to simulate a solvated carbon
nanotube. I followed the basic procedure in the NAMD Tutorial of
Ubiquitin in a Water Sphere. However, after the simulation completes, I
notice that the nanotube immediately collapses (forms an oval-ish
cylinder shape). I repeated the exercise without any water molecules
and the same thing happens. I'm wondering if there is an issue with the
bond angle rigidity. Is there a way I can tweak that? Or does anybody
have any other suggestions? Perhaps changing some parameters? Thank you.

Jonathan Lee

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