On Mon, Jun 14, 2004, James W. Caldwell wrote:
> I setup a simple test: F-O-F, linear, with a linear force constant.
> the angle energy should be zero, right? well it's 0.2 kcal/mole
> in both sander7 and sander8. I've attached a tar file with an input,
> prmtop, prmcrd and the sander8 output.
>
See the code around line 416 of ene.f, and consider changing "pt999"
to something closer to unity. Note that acos(-0.999) is 177.4 degrees,
which
is significantly from 180. There is a nasty problem involved in getting
good forces with linear bond angles. Someone should plunge in and fix the
code (similar problems arise with linear angles in ephi.f). I have a
vague recollection that moil does this "correctly", so that might be worth
checking....
....dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Apr 05 2006 - 23:50:01 PDT
