# Re: ABF application

Date: Fri Nov 09 2007 - 03:23:57 CST

Dear Jerome,

v1 will actually move approx. parallel to v rather than towards the head
of v .... And I would like the head of v1 to move towards the head of
v..... I also tried to use the distance between the two heads as the
reaction coordinate... The problem here is that this doesnt alow the

I will go on testing and see what is the best option ....

Thanks again

Jerome Henin wrote:

>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.
>Best,
>Jerome
>
>On Nov 8, 2007 9:28 AM, Vlad Cojocaru
>
>
>>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
>>
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>>
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>>
>>
>>
>
>
>

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EML Research gGmbH
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69118 Heidelberg
Tel: ++49-6221-533266
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