[gmx-users] Re: harmonic angle potential (solved)

Grace Brannigan gbrannig at physics.ucsb.edu
Tue Sep 21 02:11:51 CEST 2004

Thanks for the advice - it turned out to be an issue in my program of
calculating angles of molecules that had been "broken". I'm not sure why
the wrong answer wasn't more wrong, but it matches now.  Still, I do think
it would be helpful to specify in the chpt. 4 of the manual that the
harmonic calculation is done in radians - its sort of misleading since one
enters in the equilibrium angle in degrees.

Also, I don't think it should be a problem to have an equilibrium angle of
180 - the force should vanish, not have a singularity. I know numerically
there might be an issue, but from looking at the angles function it seems
Gromacs checks for that...

Again, thanks for the input,


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