[gmx-developers] Implementation of Urey-Bradley
David van der Spoel
spoel at xray.bmc.uu.se
Mon Feb 6 08:52:21 CET 2006
Mark Abraham wrote:
> 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
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....
> Mark Abraham
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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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