Re: Two dimensional ABF

From: Branko (
Date: Tue Jun 11 2013 - 12:38:19 CDT

Possible solution is to find atom near A for which you know, from
previous unbiased runs, that move similar to A and to chose this atom
for distance. In peptides it is not too complicated, and dihedral
implicate that you probably work on peptide. Also explain 'constraint'
for ABF-1. If you apply constrains on atoms, it have no sense to apply
force on the same atoms.


On 6/11/2013 6:33 PM, Nadeem A. Vellore wrote:
> 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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