From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jun 11 2013 - 12:35:52 CDT
Hi Nadeem,
The approach you outline with oneSiteSystemForce is basically correct, but you need to apply it to the dihedral variable: define that as G-F-E-A and set oneSiteSystemForce there too. So you'll be measuring forces only on sites B and G, neither of which is affected by biases on the other variable.
Best,
Jerome
----- Original Message -----
>
>
> Dear All,
>
>
>
> I am trying to use ABF using two collective variables and through the
> ABF documentation it was implied that the collective variables
> should be orthogonal.
>
> Here the detail about my system
>
>
>
> ABF-1 : distance constraint between A and B
>
> A-B
>
>
>
> ABF-2 : dihedral
>
> A-E-F-G
>
>
> In my case I have same definition of atoms in group1 in both
> collective variables. Is this something not correct for orthogonal
> definition. Should I be using the "oneSiteSystemForce" option and
> redefine my distance as B-A (group1 now being B) to circumvent this.
>
>
>
> I want to check this before I start the simulation runs. Any comment
> will be useful.
>
>
>
> Thanks
>
> Nadeem
>
>
>
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