[gmx-developers] Implementation of Urey-Bradley

[David van der Spoel]

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....
> 
> Regards,
> 
> Mark Abraham
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-- 
David.
________________________________________________________________________
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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