4.1. CHARMM Angle¶
4.1.1. Functional Form¶
The CHARMM angle potential has the functional form:
\(E={{K}_{a,ijk}}{{\left( {{\theta }_{ijk}}-{{\theta }_{0,ijk}} \right)}^{2}}+{{K}_{ub,ik}}{{\left( {{R}_{ik}}-{{R}_{ub,ik}} \right)}^{2}}\)
The force-field parameters for this potential and units are given by:
Equation Symbol | Parameter Definition | Units |
\(K_{a,ijk}\) | Angle coefficient for atoms [i,j,k] | energy/degrees^2 |
\(\theta_{0,ijk}\) | Equilibrium angle for atoms [i,j,k] | degrees |
\(K_{ub,ik}\) | Coefficient for Urey-Bradley potential [i,k] | energy/length^2 |
\(R_{ub,ik}\) | Equilibrium bond length for Urey-Bradley potential [i,k] | length |
4.1.2. XML Schema¶
The XML schema for the CHARMM angle 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 |
Angle coefficient for atoms [i,j,k] | \(K_{a,ijk}\) | Ka |
Equilibrium angle for atoms [i,j,k] | \(\theta_{0,ijk}\) | Theta0 |
Coefficient for Urey-Bradley potential [i,k] | \(K_{ub,ik}\) | Kub |
Equilibrium bond length for Urey-Bradley potential [i,k] | \(R_{ub,ik}\) | Rub |
The general attributes (describing the entire data set) are given by:
General Attributes | Cardinality | Value/Definition |
style | Fixed | CHARMM |
formula | Fixed | Ka*(Theta-Theta0)^2+Kub*(R-Rub)^2 |
Ka-units | Required | Enumerations specified in schema |
Theta0-units | Required | Enumerations specified in schema |
Kub-units | Required | Enumerations specified in schema |
Rub-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
Specific Attributes | Cardinality | Value/Definition |
precedence | Optional | Precedence of parameter set (where specified) |
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.