Re: ABF application

From: Jerome Henin (
Date: Thu Nov 08 2007 - 14:42:58 CST

Dear Vlad,
I am not sure how to translate your idea in "theoretically correct" terms.
My feeling is that the biasing force component orthogonal to v is
arbitrary and not accounted for in the equations you will explicitly
or implicitly be using.
Have you tried simply applying the bias along v? If yes, and the
behavior is not what you expect, then what you want to do is really
add an external bias, *independent from ABF* to contain the system
within a region that you consider relevant.
I would avoid inserting that extra bias into the ABF one for clarity
and to prevent breaking things in a subtle and undetectable way.
Nothing prevents you from adding that bias using the existing
restraints or by adding a custom one to that section of the code.

On Nov 8, 2007 9:28 AM, Vlad Cojocaru
<> wrote:
> Dear Jerome, Chris, NAMD users,
> Is it possible in ABF to apply the biasing force on a different
> direction than that of the reaction coordinate?
> I was thinking to retrieve the force $force (along the reaction
> coordinate (r.c.) in the "ABForce" procedure, then in ABFapply calculate
> a new force $new_force as $force/cos(alpha) (alpha = the angle between
> the direction of the r..c. and the direction of the applied force), and
> then apply this force on the new direction (Fvec = [vecscale $new_force
> $e_dir], where $e_dir = the unit vector of this direction).... In this
> way the force acting on the r.c direction will still be $force which
> will be used for the estimation of the free energy along the r.c. ...
> Such an application would make sense if I want to define the reaction
> coordinate as the projection of one vector v1 on a defined vector v in a
> protein and then move the head of v1 towards the head of v, rather than
> parallel to v ....
> Best wishes
> vlad
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