Table 2. SMIRNOFF v0.1 format sections for nonbonded interactions.
Each section corresponds to one nonbonded force type and lists the associated XML nodes and attributes, which are unit-bearing and modify the behavior of the whole section (e.g. the coulombl4scale attribute in the NonbondedForce section controls scaling of 1–4 Coulomb interactions wherever they occur), as well as individual entries which provide details of interactions or other details of the force held (e.g. Atom entries within NonbondedForce give details of specific nonbonded parameters assigned to atoms recognized by specific SMIRKS patterns). Of the sections listed here, only NonbondedForce entries are required, alll entries list as “required” must be present for any section that is included. Full details of the format detailed above are available online at https://github.com/openforcefield/openforcefield/blob/0.1/The-SMIRNOFF-force-field-format.md (visit the main openforcefield repo for links to the current format if it has changed since this writing);Figure 4 shows an example of how it is used.
| NonbondedForce | ||
|---|---|---|
| Section attributes | ||
| attribute | description | required? |
| coulomb14scale | Coulomb scale factor for 1-4 interactions | yes |
| lj14scale | LJ scale factor for 1-4 interactions | yes |
| sigma_unit | Units for sigma or rmin_half | yes |
| epsilon_unit | Units for epsilon or rmin_half | yes |
| Section nodes are Atom entries | ||
| attribute | description | required? |
| SMIRKS pattern with one indexed atom | yes | |
| rmin_half | LJ distance parameter as rmin/2 | yes, or σ |
| sigma | LJ distance parameter as σ | yes, or rmin/2 |
| epsilon | LJ interaction parameter as ϵ | yes |
| GBSAForce | ||
| Section attributes | ||
| attribute | description | required? |
| gb_model | Selected GB model | |
| solvent_dielectric | dielectric constant for solvent | yes |
| solute_dielectric | internal dielectric for solutes | yes |
| radius_units | Units for radii | yes |
| sa_model | surface area model | yes |
| surface_area_penalty | unit-bearing value for surface area penalty | yes |
| solvent_radius | solvent radius with units | yes |
| Section nodes are Atom entries | ||
| attribute | description | required? |
| smirks | SMIRKS pattern with one indexed atom | yes |
| radius | GB radius | yes |
| scale | GB scale parameter | yes |
| BondChargeIncrement | ||
| Section attributes | ||
| attribute | description | required? |
| method | Base charging method, e.g. AM1 | yes |
| increment_unit | units used for bond charge corrections | yes |
| Section nodes are BondChargeIncrement entries | ||
| attribute | description | required? |
| smirks | SMIRKS pattern with two indexed atoms | yes |
| increment | increment to move from first indexed atom to second | yes |
| Constraints | ||
| Section attributes | ||
| None | ||
| Section nodes are Constraint entries | ||
| attribute | description | required? |
| smirks | SMIRKS pattern with two indexed atoms to constrain | yes |