Date: Wed Sep 28 2011 - 17:35:12 CDT
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.
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