AMBER: Questions toward Azobenzene

From: Chih-Ying Lin <chihying.usc.edu>
Date: Thu, 27 Mar 2008 21:23:40 -0700

Hi
Can N=N double bond rotate freely?
Can N=N double bond rotate freely under minimisation?

I am using Amber to run the cis-azobenzene minimisation. There are two states for running the minimisation.
Minimisation Stage 1 - Holding the solute fixed => visually, it is still a cis-azobenzene
Minimisation Stage 2 - Minimising the entire system => visually, it become a trans-azobenzene, but still have different
structrure with real trans-azobenzene

I don't know how this happened after 2nd minimisation.


Any ideas about this?

Thanks


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Received on Fri Apr 18 2008 - 21:14:38 PDT
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