[gmx-developers] Small hack regarding dihedrals

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 25 14:25:26 CEST 2013

I forget which, but you will anyway need a test case that shows you
that your modification is working correctly. Make a small but relevant
system and use it with mdrun -rerun to compute single-point energies
and forces. Then hack functions one by one by forcing them to output
zero until you see an effect with mdrun -rerun. Now you know what
function to work on, and have your test machinery ready to use!


On Wed, Sep 25, 2013 at 2:15 PM, MURAT OZTURK <murozturk at ku.edu.tr> wrote:
> Hey guys,
> I am trying to introduce a small hack that will  turn off dihedrals if the
> middle bond is longer than a threshold.
> It should be as simple as
> midDist= iprod(r_jk,r_jk)
> midDist *= gmx_insqrt(midDist)
> if ( midDist > threshold)  {don't even bother calculating anything for this
> dihedral}
> else {continue as usual}
> But there are so many functions in bondfree.c. I need to locate that is
> responsible for regular, periodical dihedrals (type 1). Which one is this?
> My suspects are..
> dopdihs, dopdihs_XXXX (noener etc.) , pdihs, pdihs_XXXX (noener etc.)
> Is there any documentation I can look at to figure our what these do? There
> are not many comments within the code.
> I appreciate the input. This is all for a fancy coarse grained system.
> Murat
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