From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Nov 13 2007 - 09:39:43 CST
Dear Jerome, NAMD users,
I thought that the best option would be to introduce the component of
the bias orthogonal to the direction of the reaction coordinate via an
external tcl script while the ABF bias will be added on the r.c
direction. However, in the ABF manual, its written that one should not
call TclForces in the NAMD config file while running ABF. Could you
give me a short hint about how should I invoke such tcl script while
running ABF?
And a second short question: I would like to add this additional bias
only at the time steps when the ABF bias is apllied. How could I check
if in the next time step an ABF bias will be applied (since
"fullSamples" > 0, the ABF bias will not be applied continuously)?
Thanks for any ideas
Best wishes
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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