8.7. Non-Bond Lennard-Jones GROMACS Potential¶
8.7.1. Functional Form¶
The non-bond Lennard-Jones GROMACS potential has the functional form:
\(E = 4 \cdot {\epsilon} \cdot \left[ {\left( \frac {\sigma}{R_{ij}} \right)^{12} - \left( \frac {\sigma}{R_{ij}} \right)^{6}} \right] + {S_{LJ}}\left({R_{ij}}\right)\)
The force-field parameters for this potential and units are given by:
Equation Symbol | Parameter Definition | Units |
\(\epsilon\) | Potential well depth for atom [i] | energy/mol |
\(\sigma\) | Interatomic cut-off distance for atom [i] | length |
8.7.2. XML Schema¶
The XML schema for the non-bond Lennard-Jones GROMACS 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] | (implicit) | AtomType |
Potential well depth for atom [i] | \(\epsilon\) | epsilon |
Interatomic cut-off distance for atom [i] | \(\sigma\) | sigma |
Inner cut-off distance for atom [i] | r_1 | |
Outer cut-off distance for atom [i] | r_cut |
The general attributes (describing the entire data set) are given by:
General Attributes | Cardinality | Value/Definition |
style | Fixed | Lennard-Jones (12-6) |
formula | Fixed | 4*epsilon*[(sigma/R)^12-(sigma/R)^6] + S_LJ(R) |
epsilon-units | Required | Enumerations specified in schema |
sigma-units | Required | Enumerations specified in schema |
r-units | Required | Enumerations specified in schema |
The specific attributes (attached to each set of parameters) are given by:
Specific Attributes | Cardinality | Value/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.