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.
Chris. -- 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 description. http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png -- Thanks and Regards, kartheek, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
