[gmx-users] Porting CHARMM topologies and parameters

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 18 08:47:44 CEST 2006

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 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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