I’m a bit confused. In angle style harmonic, with a positive k, is chain stiffness favored (i. e. “bending” suppressed) by an equilibrium angle (theta_0) of 0 degrees or 180 degrees? Having looked at the code for angle_harmonic.cpp, the answer depends on the order of atoms in anglelist. In the code, lines - are:
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
Is i2 the “middle atom” of the angle? If so, that would seem to make the answer 180 degrees, which makes sense. I’m getting some strange prelim results, though, so I wanted to make sure.
Thanks,
Rob