hi folks,
i'm a little stuck in the question whether the order of atom indices
(a1-a2-a3-a4 or a4-a3-a2-a1) plays any role when defining an
additional/new proper dihedral. as usual, i utilize the amber99sb force
field.
for the computation of the potential, the order shouldn't play any role,
since cos(phi)=cos(-phi), where phi is the dihedral under consideration.
however, for the calculation of the potential's derivative and therefrom
for forces, i would expect a crucial difference due to the differing
sign of phi. are my worries reasonable or is there some
algorithmic/mathematical dodge circumventing that issue?
would someone please shed a little light on the dark! thanks in advance,
vedat
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