Re: CNT modeling

From: Cesar Luis Avila (
Date: Tue Jun 12 2007 - 16:05:21 CDT

Have you tried the following tutorial?

Jonathan Lee escribió:
> 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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