[gmx-developers] Small hack regarding dihedrals

[Erik Lindahl]

Type 1 is a "proper dihedral", which means "do_pdihs()" ;-)

However, beware if you are running in parallel with domain decomposition - even if _you_ won't evaluate the interaction when it is beyond the cutoff, Gromacs will complain if it cannot communicate the coordinates for you. 
Cheers,

Erik

On Sep 25, 2013, at 2:25 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> 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!
> 
> Mark
> 
> 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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