[gmx-users] Porting CHARMM topologies and parameters

[David van der Spoel]

Mark Abraham wrote:
> 
> It's 5, actually, there are cross-bond-bond and cross-bond-angle 
> functions at 3 and 4, neither of which make it into Table 5.4. You can 
> see this working in the source code of src/gmxlib/ifunc.c.
> 
> The advantage of actually using this function type is that you get a 
> separate energy term for U-B, rather than having it split over a 
> harmonic angle and a harmonic distance potential, (which will have other 
> contributions in the former case) which is much better for testing the 
> implementation against another CHARMM implementation. It'd be moot for 
> production calculation, however.
Thanks for pointing that out. I've updated the table in the CVS version 
of the manual.

-- 
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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