Re: A question about restaints force.

From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Fri Apr 25 2008 - 17:48:40 CDT

Unless you want something fancy, free energy restraints should be
enough.
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node34.html
Victor

On Fri, 2008-04-25 at 17:17 -0400, Gungor Ozer wrote:
> The answer to your question is TCL forces, where you can apply varying
> forces that you could update at each step.
>
>
> http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/10Ala-tutorial-files.tar.gz
>
>
> That tutorial might be useful for a start. Please note that this is a
> constant velocity pulling at z-direction only. You might wanna modify
> your force vector as you wish (using coordinates of the two particular
> atoms you were mentioning).
>
>
> Hope that'll help...
> -gungor
>
>
> On Fri, Apr 25, 2008 at 4:23 PM, Yang Gao <yanggao_at_iastate.edu> wrote:
> Dear all,
>
> I want to apply an restaint force between two atoms during
> NAMD run, just
> adding a external force in the line that connect the two
> atoms, but change
> nothing else. I have searched tutotials but just find in SMD
> how to define a
> constant velocity or force pulling in a fixed direction. But
> as the atoms may
> change their direction during runtime, this may not suitable
> for my case. I
> hope some of you may know the codes for define the specific
> interation or
> modify the SMD code to change the direction of the force
> during runtime.
>
> Thank you very much.
>
> Gao, Yang
>
>
>
>
>
>
> --
> -gungor

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