From: Collin Nisler (cnisler_at_uchicago.edu)
Date: Wed Oct 19 2022 - 12:04:15 CDT
Hello all, I have an RNA system that contains two structured "arms" that form a ~45 degree angle in their starting configuration. We have experimental evidence to suggest that the ends of the two arms interact, and I have a model of this final configuration in which there are six specific Watson-Crick base pairs between an overhang at the end of one arm and a loop at the end of the other arm.
I want to use targeted MD to drive the simulation from the initial structure to the final configuration, but I've seen in the mailing list that colvars is suggested over TMD. In this particular instance, to try and form this specific interaction, would colvars be appropriate, and is there a general recommendation for how I would define the colvars to form these interactions? Thanks in advance.
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