Re: Dangling Bonds?

From: Axel Kohlmeyer (
Date: Wed Sep 28 2011 - 17:58:18 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 sp2.
>   Are there any techniques or work-arounds to deal with this? Thank you for
> your time.

whether you get an sp2 or sp3 type geometry depends entirely on the
force field (and thus is independent of NAMD itself). if you apply parameters
for an sp3 carbon to a radical, then your input is not correct.
you will need to reparameterize those atoms unless somebody
has already done it.

however, you also have to keep in mind, that NAMD does classical
MD, so your radical is completely "non-radical", i.e. it cannot react
or in any way and that may not be a good model in the first place.



Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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