Welcome to metallicious’s documentation!

metallicious is an automated tool for creating force fields for metal-containing systems with a covalent model of the metal. By utilizing a library of templates, metallicious identifies the template that matches the metal site in the structure. It copies the bonded parameters from the template and performs charge redistribution to account for charge transfer. In cases where no suitable template is found, metallicious automatically performs parameterization.

Limitations: The code currently supports organometallic structures with metals separated by at least 2 non-metal atoms. Metal clusters are not supported. Additionally, metals of the same type must have the same charge and multiplicity.

Note

This project is under active development.

Contents

• Installation
  • Dependencies
• Usage
  • Python module
  • Quick start
    • Initial topology file
  • Handling missing templates
    • 1. Parametrize template
    • 2. Truncate existing template
    • Input for supramolecular_structure class
  • Bash command line
  • Available parameters
    • Default templates
    • Lennard-Jones
• Examples
  • Example 1: Quick start
  • Example 2a: Automated initial force-field parameters
  • Example 2b: Different formats
  • Example 3: Homoleptic cage
  • Missing templates
  • Example 4: Parametrization of new template
  • Example 5: Truncation schemes
• Tutorials
  • Tutorial 1: Force-field parameters from SMILES string
  • Tutorial 2: Parametrization of template for gallium cages (known issue and solution)
  • Tutorial 3: Using custom template
  • Tutorial 4: Custom template library
  • Tutorial 5: GROMACS tutorial for MD simulations of metallorganic structures from scratch
  • Tutorial 6: Host-guest complex parametrization