VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
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
script:
https://github.com/colvars/colvars/blob/master/vmd/scripts/colvar_display.tcl

Best,
Jerome

On 13 February 2017 at 11:32, Mehdi Bagherpour <mehdi.bpour_at_gmail.com>
wrote:

> 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
>