Assigning a Force Field

Prepare or import a simulation model. DFF can be used to build three-dimensional cubic liquid boxes and liquid interfaces, though this functionality is intended primarily for parameterization and validation. For complex molecular systems, an external software package may be used to build the simulation models. DFF supports most popular file formats, including .pdb, .mol2, and .car files.

It is important to maintain a consistent assignment of topologies and formal charges in order to assign atom types. If atomic coordinates are provided with reasonable precision, DFF can automatically assign topologies and formal charges.

Once topologies and formal charges are assigned, the next step is to assign atom types and force field parameters using TEAMFF. Multiple force fields of the same type can be used together, but they are called in the order specified. All valence parameters for a given molecule must come from one force field; intra-molecular parameters cannot be mixed across force fields. Only inter-molecular parameters (nonbond terms) may be combined from different force fields using the combination rule. In practice, DFF scans all molecules against the selected force field. If any parameters are missing for a molecule, it is not assigned and is passed to the next force field in the list.

When all parameters are found, the atom types and parameters—possibly sourced from different force field tables—are unified into one consistent force field for the simulation model. A new set of atom types corresponding to this unified table is automatically generated and assigned to the simulation model. The model and the unified force field can then be used directly in simulations.

If parameters are still missing, TEAMFF will report the missing terms, which can be used for parametrization.