Re: ABF - changing the reaction coordinate

From: Jerome Henin (
Date: Fri Jul 06 2007 - 10:54:02 CDT

Hi Per,
The force should be applied along the gradient of the RC, which is a linear
functional, so in this case the gradient would be the difference of the
gradients for each of the atom-atom distances. How the code would look
depends on how exactly you implemented the rest.

I admit I am struggling to refrain from asking with what kind of force field
you describe proton transfer in NAMD...

On Friday 06 July 2007 11:18, Per Jr. Greisen wrote:
> Hi all,
> I would like to use the ABF in order to estimate energy along a proton
> transfer reaction. So I have the defined the reaction coordinate as z =
> r(D-H)-r(A-H). I have changed the vectors in tcl-script distance.tcl but I
> am very much in doubt how to change the last part where one has to aplly
> the forces(proc ABFapply):
> addforce $abf1 [vecinvert $F2]
> addforce $abf2 $F2
> return $force
> should the force be along the r(D-H) equivalent to $abf1? Or help or
> advise appreciated. Thanks in advance
> Best Regards
> Per

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