[gmx-developers] Implementation of Urey-Bradley

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 24 09:00:54 CET 2006

Mark Abraham wrote:
> 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.
Thanks Mark,

I will do that.

> Mark
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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