> And the one in Rappé's paper (after Towhee's correction):
> Triangular (UFF paper) -> K_ijk/9 ( 1 - cos(3t))
> Those two expressions are not equivalent. Even more they differ a lot. A
> simple plot would tell you that. They both have a minimum at 120 deg.
> Nevertheless Rappé's version contains a minimum at 0. I agree with OB
> implementation that this is not at all true but I want to know the origin of
> the expression you have used.
So your question spurred me to do a little reading. The ESFF, which was
developed as a similar rule-based force field to UFF, but modified Rappe's
angle potential with an exponential penalty if the angle was small. AFAIK these
two (UFF and ESFF) are the only published rule-based force fields:
1. Shi, S., Yan, L., Yang, Y., Fisher Shaulsky, J. & Thacher, T. An
extensible and systematic force field, ESFF, for molecular modeling of organic,
inorganic, and organometallic systems. J. Comp. Chem. 24, 1059–1076 (2003).
I've modified the current git master with this penalty and it seems to work
well. What do you think of this?
// ka already is pre-computed as ka/n^2 to save CPU cycles
energy = ka * (1 - cos(n*theta)) + exp(-20.0*(theta - theta0 + 0.25));
It might be slightly slower, but for most angles, it recovers the form
suggested by Rappe while preventing angles less than theta0 - the 0.25 is an
empirical fudge to make sure the exponential decays to zero near theta0.
-Geoff
------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
