From: Jérôme Hénin (
Date: Tue Feb 14 2017 - 08:36:11 CST

Dear Mahdi,

That sounds like a difficult problem. What I recommend is loading
structures of relevant complexes into VMD and trying out various collective
variables using the VMD interface of the colvars module and perhaps this


On 13 February 2017 at 11:32, Mehdi Bagherpour <>

> Dear VMD users:
> I am going to use the adaptive biasing sampling (ABF) for getting free
> energy landscape of protein-DNA affinity. For this reason I am going to
> pull the protein along the helical axis as the protein always stays on
> major groove. In fact, while protein moves along DNA helical axis,
> simultaneously there is a rotation along this axis that keep protein on
> major groove.
> Question is, does anybody has a suggestion how can I choose the collective
> variables?
> Cheers,
> Mahdi