Hi,
On May 4, 2006, at 4:19 AM, gil claudio wrote:
Thanks for the help, Erik and David.
Does this mean that when invoking rb dihedrals, the
real equation being used is
RB(phi) = C0 - C1 cos(phi) + C2 cos^2(phi) - C3
cos^3(phi) + C4 cos^4(phi) - C5 cos^5(phi)
Yes, if you convert it to biochemistry convention. In the code the
angle is converted to polymer convention instead.
See equation 4.61, and note the following line where it says
psi=phi-180.
It might be good to mention this convention in the
manual.
I count at least three places where it is already mentioned in the
section when we define RB-dihedrals and the conversion from OPLS
parameters on pp 55-56, and an explicit note about the effect on the
sign of C_n terms. ;-)
Cheers,
Erik
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