[gmx-users] Question regarding dihedral angle parameters

[Upendra N]

Dear Justin
Thank you very much.

Yours sincerely
Upendra N



On Thu, Aug 16, 2018 at 8:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/16/18 10:52 AM, Upendra N wrote:
>
>> 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)
>>
>
> Have a look at any primary reference for a paper that derives force field
> parameters; you'll find ample examples.
>
> Also remember that a dihedral potential is not a real physical force. It's
> a band-aid for inaccuracies in nonbonded interactions (primarily 1-4
> interactions). As you rotate about a bond, you're computing the potential
> energy of the molecule, hence asymmetry of the profile in many cases.
> Dihedral terms are added into the potential energy equation to get the
> correct profile (or as close to it as possible).
>
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
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