Automatic Parameters

DFF has the functionality to make automatic parameters for two purposes: to provide initial parameters for fitting and/or to provide default parameters used to approximate force field. Similar to the methods used in UFF force field [^1], automatic parameters are calculated based on a set of base parameters specified for default atom types. The force field parameters for bond stretches, bond angle and torsion angle distortions, out-of-plane angle distortions, and VDW parameters are calculated based on a set of rules.

The base parameters are stored in the file AtomType.dat, which is located in the Data directory. You can modify parameters through the user interface or by directly editing the data files.

Bond Stretch

Two variables - reference bond length and force constant are calculated:

where is the bond radii of atom i and is the effective charge of atom i, both are basic atomic parameters.

Bond Angle Distortion (i-j-k)

Three variables are calculated: reference equilibrium angle, force constant and multiplicity of energy minima. The force constant is:

where

The multiplicity n and the reference equilibrium angle are fixed depending on the preferred geometry of the central atom type j:

Dihedral Angle Torsion (i-j-k-l)

Three variables are calculated: reference torsion angle, energy barrier height and multiplicity of energy minima. The torsion energy barrier height is:

where , are intrinsic torsion barrier parameters for atoms j and k and is the total number of torsion angles about bond (j-k). The multiplicity n and the reference torsion angle are determined by the preferred geometries of center atoms j and k:

Out-of-Plane Distortion (i-j-k-l, where j is the central atom)

Out-of-Plane distortion is defined only when the preferred geometry of atom j is PYRAMIDAL or PLANAR. The reference angle is always 0.0, and force constant is 0.0 or 5.0, respectively.

Lenard Jones Potential

Two parameters: the VDW well depth and diameter in term of the Lennard-Jones 12-6 function are provided as basic atomic parameters. The parameters are taken or transferred from literature or previous research work.

Atomic Charges

The atomic charges are estimated using the QEQ method.[^2]. The basic parameters used to calculate charge distribution are the ionization potentials (IP) and electron affinities (EA) of relevant atoms, which are collected from literature and saved in the Elements.dat file.

[^1] Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. UFF, a full periodic table forcefield for molecular mechanics and molecular dynamics simulations. Journal of the American Chemical Society 1992, 114, 10024-10035. [^2] Rappe, A. K.; Goddard III, W. A. Charge equilibration for molecular dynamics simulations. The Journal of Physical Chemistry 1991, 95, 3358-3363.