[gmx-users] Question regarding dihedral angle parameters

[Upendra N]

Dear Justin
Thank you very much. I also would like to understand why the nature of the
potential energy is complex and its origin.
Kindly suggest me some reference that contains many examples (i.e different
combination of atom types and associated torsional profiles)
Thank you in advance

Yours sincerely
Upendra N



On Thu, Aug 16, 2018 at 5:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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