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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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