[gmx-users] Polymer Dihedral Angle Definition

[Justin Lemkul]

On 1/14/14, 3:34 PM, decaiyu wrote:
> Dear All,
>
> When I look at the dihedral angle definition (see below) for gromos43a1
> force field, most equilibrium angles are either 180 or 0 degrees.
> I assume that the second number represent the strength of dihedral angle
> term and the third one is the power.

More specifically, force constant and multiplicity.

> How do I define the gd term involving a tetrahedral structure, such as
> C-C-N-(C3). The equilibrium angle here is not 180 or 0 degree. How do I
> decide the value for the second and third term?
>

By doing proper parametrization according to the methods of your chosen force field.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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