From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Nov 13 2007 - 11:52:53 CST
Dear Jerome,
Thanks a lot for answering ... I hope one day I will have the chance to
make it up to you
I tried to define different reaction coordinates but till now I didnt
come up with a better idea ....
I will give it a try with a customized restraint ....
I would add the restraint only when the ABF bias is applied because than
the resulting bias (ABF + restraint) would give me exactly the direction
of the external force I want but still keeping the samples in which no
external force is added to the system .... I am not sure whether this
makes sense ...
Thanks again,
Best
vlad
Jerome Henin wrote:
>Vlad,
>I tried to answer you questions below. I should add that I am still
>wondering whether your problems might be solved by using a more
>appropriate variable as a reaction coordinate...
>
>On Nov 13, 2007 10:39 AM, Vlad Cojocaru
><Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
>
>
>> 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?
>>
>>
>
>You can't define a separate script, so my suggestion is to add a
>custom restraint to the existing ones in the ABF code. There are two
>routines involved: restraints_init and restraints, towards the end of
>the file abf_script.tcl. You need to add a section in each of these.
>Hopefully the existing restraints will provide a clear template.
>
>
>
>> And a second short question: I would like to add this additional bias only
>>at the time steps when the ABF bias is apllied.
>>
>>
>
>I don't know why you would do such a thing...
>
>
>
>>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)?
>>
>>
>
>One thing you could do is to add a parameter to the "restraints"
>procedure, saying whether or not an ABF bias is being applied.
>
>Jerome
>
>
>
>> 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
>>----------------------------------------------------------------------------
>>
>>
>>
>>
>>
>
>
>
-- ---------------------------------------------------------------------------- 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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