[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine

[bipin singh]

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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Thanks and Regards,
kartheek,