Re: Dangling Bonds?

Date: Thu Sep 29 2011 - 08:45:39 CDT

On Wed, Sep 28, 2011 at 6:35 PM, <> wrote:
> Hello All,
> I am curious if there is any way that NAMD can handle dangling bonds, or
> free radicals.
> For instance, if you bond carbon to three neighbors, it will take on the
> 2D planar sp2 configuration. If you break the double bond and create a
> dangling bond, it should conform into a 3D tetragonal sp3 configuration.
> However, I cannot find anyway to do this with NAMD, except by possibly
> capping the dangling bond with a hydrogen (which I strongly do not wish to
> do). Thus, my problem is three carbon neighbors will always result in

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