Hi all, I am studying a system which consists of DNA duplex 20 base pairs. Actually I am interested in studying the base flipping of the thymine. I have the crystal structure of extrahelical DNA in which thymine is out side the helical structure. I want use pulling simulations to bring this base from extrahelical to Intrahelical conformation, is there any way to do it in GROMACS pull code. Please see the figure below (link) for description. http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png
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