4. Molecule Type

This section present first the structure of the Molecule Type object. Then, how to initialized a MT and how to assigned molecule of the topology file to this MT.

The SingleMolecule object is presented, but this part is adressed to advance user.

Finally it summarized the available MT.

• 4.1. How to create MT
  • 4.1.1. Initialization
  • 4.1.2. Define Diagram
  • 4.1.3. Optical Analysis
  • 4.1.4. End the definition
• 4.2. Molecule Type structure
  • 4.2.1. Core information
  • 4.2.2. Internal information
  • 4.2.3. Molecule Type Parameter
  • 4.2.4. List of the molecule
  • 4.2.5. Single Molecule Object
  • 4.2.6. Diagrams
• 4.3. Single Molecule Parameter
• 4.4. Available MT
  • 4.4.1. Solvants
  • 4.4.2. Ions