[gmx-users] Question regarding dihedral angle parameters
nupendra90 at gmail.com
Thu Aug 16 18:06:08 CEST 2018
Thank you very much.
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
>> 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 A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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