[gmx-users] form of the angle potential in ffgmx2bon.itp

[Markus O Kaukonen]

Dear all,

What is the meaning of angle terms in ffgmx2bon.itp ?
(this is option 1 in pdb2gmx)

>[ angletypes ]
>  ; i    j    k func       tHC         cth
>   HO   OA    C    1   109.500     397.480
>   HO   OA   C1    1   109.500     397.480

So is the angle energy, for example, for HO-OA-C triplet

A) 0.5*397.480*(current_angle_in_deg - 109.500)^2  [kJ/mol]

or is it

B) 0.5*397.480*(cos(current_angle_in_deg) - cos(109.500))^2  [kJ/mol]

or

C) something else ?

I get the impression from the manual 3.1.1 that it should be option A) but
test calculations give strange results.

Best Wishes, Markus



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