[gmx-users] Question regarding dihedral angle parameters
jalemkul at vt.edu
Thu Aug 16 17:29:47 CEST 2018
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 A. Lemkul, Ph.D.
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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