[gmx-users] Question regarding dihedral angle parameters

[Justin Lemkul]

On 8/16/18 4:16 AM, Upendra N wrote:
> Dear Gromacs users,
>
> I am a beginner in gromacs. I was trying to understand how dihedral terms
> are used and I noticed that for Amber99 ff the ffbonded.itp files have
> mutliple dihedral parameters for the same dihedral type, each with
> different force constant, multiplicity and phase angle
>
> For instance,
>
>   CT  OS  CT  OS    9       0.0      0.41840     3  ; Junmei et al, 1999
>   CT  OS  CT  OS    9     180.0      3.55640     2  ; Junmei et al, 1999
>   CT  OS  CT  OS    9     180.0      5.64840     1  ; Junmei et al, 1999
>
> I am wondering what determines which of this is assigned to a given
> dihedral.
>
> Also, why is the phase shift different as I understand that phase shift
> determines where is the minima of the energy in the energy vs torsion plot.
>
> I have tried looking for the reason but somehow have not found a
> satisfactory answer. I would really appreciate if someone can clarify this
> to me.

1-D potential energy surfaces are often complex, with multiple local 
minima. The dihedral energy function is such that one can sum up terms 
with different phases and multiplicities to recover the target energy 
surface (QM).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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