Re: ABF application

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Nov 09 2007 - 03:23:57 CST

Dear Jerome,

Thanks a lot for your answer... If I apply the bias along v, the head of
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
head of v1 to move beyond the head of v ...

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

Thanks again

vlad

Jerome Henin wrote:

>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.
>Best,
>Jerome
>
>On Nov 8, 2007 9:28 AM, Vlad Cojocaru
><Vlad.Cojocaru_at_eml-r.villa-bosch.de> 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
>>
>>--
>>----------------------------------------------------------------------------
>>Dr. Vlad Cojocaru
>>
>>EML Research gGmbH
>>Schloss-Wolfsbrunnenweg 33
>>69118 Heidelberg
>>
>>Tel: ++49-6221-533266
>>Fax: ++49-6221-533298
>>
>>e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>>http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>>----------------------------------------------------------------------------
>>EML Research gGmbH
>>Amtgericht Mannheim / HRB 337446
>>Managing Partner: Dr. h.c. Klaus Tschira
>>Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>>http://www.eml-r.org
>>----------------------------------------------------------------------------
>>
>>
>>
>>
>>
>
>
>

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------

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