[gmx-users] Question regarding dihedral angle parameters

[Justin Lemkul]

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

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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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