5.1. CHARMM Dihedral¶
5.1.1. Functional Form¶
The CHARMM dihedral potential has the functional form:
\(E={{K}_{d,ijkl}}\left[ 1+\cos \left( N{{\phi }_{ijkl}}-{{\phi }_{0,ijkl}} \right) \right]\)
The force-field parameters for this potential and units are given by:
Equation Symbol | Parameter Definition | Units |
\(K_{d,ijkl}\) | Dihedral coefficient for atoms [i,j,k,l] | energy |
\(N\) | Nonnegative integer coefficient | N/A |
\(\phi_{0,ijkl}\) | Equilibrium Dihedral for atoms [i,j,k,l] | degrees |
5.1.2. XML Schema¶
The XML schema for the CHARMM 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] | \(K_{d,ijkl}\) | Kd |
Nonnegative integer coefficient | \(N\) | N |
Equilibrium dihedral angle for atoms [i,j,k,l] | \(\phi_{0,ijkl}\) | Phi0 |
The general attributes (describing the entire data set) are given by:
General Attributes | Cardinality | Value |
style | Fixed | CHARMM |
formula | Fixed | Kd*[1+cos(N*Phi-Phi0)] |
convention | Optional | Enumerations specified in schema |
Kd-units | Required | Enumerations specified in schema |
Phi0-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.