5.2. Class 2 Dihedral¶
5.2.1. Functional Form¶
The class 2 dihedral potential has the functional form:
\(E={{K}_{1,ijkl}}\left[ 1-\cos \left( {{\phi }_{ijkl}}-{{\phi }_{1,ijkl}} \right) \right]+{{K}_{2,ijkl}}\left[ 1-\cos \left( 2{{\phi }_{ijkl}}-{{\phi }_{2,ijkl}} \right) \right]\) \(\qquad +{{K}_{3,ijkl}}\left[ 1-\cos \left( 3{{\phi }_{ijkl}}-{{\phi }_{3,ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
| Equation Symbol | Parameter Definition | Units |
| \(K_{1,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{2,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(K_{3,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
| \(\phi_{1,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(\phi_{2,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
| \(\phi_{3,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
5.2.2. XML Schema¶
The XML schema for the class 2 dihedral potential has the following representation (design mode representation using Liquid XML Studio):
The relationship between the equation symbols and XML schema notations are given by:
| Parameter Definition | Equation Symbol | Schema Notation |
| Atom type of atom [i] | \(i\) | AT-1 |
| Atom type of atom [j] | \(j\) | AT-2 |
| Atom type of atom [k] | \(k\) | AT-3 |
| Atom type of atom [l] | \(l\) | AT-4 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{1,ijkl}\) | K1 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{2,ijkl}\) | K2 |
| Dihedral coefficient for atoms [i,j,k,l] | \(K_{3,ijkl}\) | K3 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{1,ijkl}\) | Phi1 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{2,ijkl}\) | Phi2 |
| Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{3,ijkl}\) | Phi3 |
The general attributes (describing the entire data set) are given by:
| General Attributes | Cardinality | Value |
| style | Fixed | Class2 |
| formula | Fixed | K1*[1-cos(Phi-Phi1)]+K2*[1-cos(2*Phi-Phi2)]+K3*[1-cos(3*Phi-Phi3)] |
| convention | Optional | Enumerations specified in schema |
| Kn-units | Required | Enumerations specified in schema |
| Phin-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
| Specific Attributes | Cardinality | Definition |
| comment | Optional | Comment attached to parameter set |
| version | Optional | Version number of parameter set |
| reference | Optional | Reference attached to parameter set |
Note that an XML document will be rejected from being entered into the WebFF database if a required attribute is left unspecified.