[gmx-users] order of atom indices regarding proper dihedrals

[Vedat Durmaz]

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