Model

A Model is a molecular system in DFF. It can be an single molecule, a set of molecules, or a macromolecule, in isolation or in a 3-D periodic condition.

Essential Data

The essential information of a model is its atomic coordinations in 3D space. In addition, connectivity of atoms, in terms of bond and bond orders, are required to completely define a model. The connectivity can be calculated if atomic coordinates are given reasonably correct.

Derived Data

The following data may be computed for a model, which are used for various purposes:

• atomic partial charges
• atom types
• group atoms
• substructure atoms
• formal charges

MSD File

Models are saved as Molecular Structure Data (.msd) file. The format of MSD file is specified in the appendix