[gmx-developers] Implementation of Urey-Bradley

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 24 06:35:18 CET 2006

David van der Spoel wrote:
> Mark Abraham wrote:
>> Hi,
>> I want to use Urey-Bradley functions in my implementation of CHARMM 
>> forcefields for gromacs. Reading the source code I see that calc_bonds 
>> in bondfree.c is where all of the bonded interactions are calculated, 
>> and that the urey_bradley C function will be called when the topology 
>> stipulates a U-B function. However that function will issue a fatal 
>> error because of line 761 of src/gmxlib/bondfree.c:
>>   gmx_impl("Not implemented yet");
>> Having read through the remainder of the function, it appears to be 
>> doing sensible things, but I haven't checked the algebra for the force 
>> decomposition yet.
>> Why does someone think this is not implemented yet? What remains to be 
>> done/tested?
> Maybe I forgot to take it out, please do and recompile. This probably 
> means that the function was never tested, so please do that carefully....

I've now done so. I have numerical agreement of energies (& components 
thereof) calculated with CHARMM27 force field using Accelrys CHARMm, my 
implementation of that force field using gromacs 3.3, and a spreadsheet. 
I can't verify the forces directly, but the gromacs algorithm looks 
correct and the endpoints of energy minimizations look to be the same 
gross state. Thus, I'd suggest removing this comment.


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