Force Field

A force field is an algorithm that is used to calculate potential energy for the modeled compounds. In JMolecular Energy the force field is represented with ForceField abstract class where all the force fields should extend this class. The class offer methods that is intended to contain certain functionalities.

Assigning Parameters

Empirical force fields most of the time assign parameters to the molecule based on the functional groups and atoms it has. This will facilitate calculating the potential energy for the molecule in the next step. Assigning parameters can be done using this method

mmff.assignParameters(atomContainer);

Energy Component

Each ForceField contains one or more of the EnergyComponent. These components are intended to address different energy terms such as bond stretching, angle bending and intermolecular interactions. Each one contribute to the total potential energy of the system by certain energy. The class ForceField sums up this energy in the double calculateEnergy(IAtomContainer) method and return it as a double. You can access the energy components in a certain force field using the method List<EnergyComponent> getEnergyComponents() which returns a list of energy component. The ForceField class is flexible and you can add or remove EnergyComponent using the method addEnergyComponent(EnergyComponent) and removeEnergyComponent(EnergyComponent). This allows for example to convert a force field into inter- or intra-molecular interactions only which is very helpful when using the force field in a docking or 3D QSAR algorithm.

Energy components can be used alone to calculate the potential energy term alone as they have their double calculateEnergy(IAtomContainer) method. The implementations also have methods to calculate energy for a certain pair of atoms for example.

Energy Unit

The ForceField use the kcal/mol unit by defualt. In case you want to calculate the energy in different unit you can use the setEnergyUnit(EnergyUnit) method for changing the unit. For example:

forcefield.setEnergyUnit(EnergyUnit.KJ_PER_MOL);//for kilojoules/mol

Cutoff Distance

In some force fields it is possible to specify a cutoff distance that defines the distance in angstrom which beyond it any non-bonded interaction will be disregarded. Using this functionality is very helpful in case of large systems where the number of intermolecular interaction is very high. The energy beyond certain distance is very small and have no significant amount and therefore can be disregarded.

forcefield.setCutoffDistance(12);//sets the cutoff distance to 12 Å

Dielectric Constant

Some force fields also has the dielectric constant functionality. This option enable us to simulate the effect of certain solvents on the degree of intermolecular interaction without the need the having the solvent molecules being modeled explicitly. The solvent is represented as a continuous media rather than individual molecules. You can modify the dielectric constant using setDielectricConstant(double) method.