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

Christopher Neale chris.neale at mail.utoronto.ca
Tue Sep 18 04:52:46 CEST 2012

You can do this with the pull code. To do so, you need to define some sort of order parameter for which you have the base flipped in at one extreme and the base flipped out at the opposite extreme. There are lots of ways to do this and, unfortunately, there is no way to know what the best order parameter is without first evaluating it. Therefore, I suggest that you start with something simple like the distance between the NH of thymine and the NH of the paired guanine (assuming that you really have a TG pair). To pick the atom pair for the distance restraint, you can ideally look at a structure of equilibrium close association and find a pair of heavy atoms that are close.


 -- original message --

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

Thanks and Regards,

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