Extension available for semi-empirical calculations with xtb

General Discussion
1

Hi everyone,

Just wanted to announce that the avo_xtb extension for Avogadro 2 is now available to download and use. :smiley:

You should see it in the plugin manager, or it can be downloaded from GitHub at the above link. It is currently a beta release really, so if anyone uses it and has bugs, feedback, or suggestions I would welcome them!

This extension adds an interface to the xtb program in Avogadro 2, enhancing it with fast but reliable calculation capabilities for simple procedures. First and foremost this means it succeeds in giving qualitatively correct geometries in situations where force fields usually fail, like ferrocene or systems where intermolecular forces are important.

Some further info:

xtb

xtb is developed by the Grimme group in Bonn and carries out semi-empirical quantum mechanical calculations using the group’s extended Tight-Binding methods, referred to as “GFNn-xTB”.

These methods provide fast and reasonably accurate calculation of Geometries, Frequencies, and Non-covalent interactions for molecular systems with up to roughly 1000 atoms, with broad coverage of the periodic table up to Z = 86 (radon).

Capabilities

This extension currently provides functionality to run the following calculation types and view the results directly in Avogadro:

  • single point energies
  • geometry optimizations
  • vibrational frequencies
  • molecular orbitals
  • molecular dynamics
  • conformer searches (via crest)

There is also the option to submit a custom command to xtb, permitting any calculation to be run, though the output is in this case only parsed for results of the basic calculation types.

Requirements

Currently, the extension does not download the xtb binary automatically, and they are not bundled with Avogadro. xtb (and crest for conformer searches) must be obtained separately. There are three options that will make xtb visible to the extension:

  1. Install xtb with conda from conda-forge and start Avogadro within the conda environment
  2. Download the xtb binary and put it into the system PATH
  3. Download xtb and place it entirely within the Avogadro/commands/avo_xtb/ directory

Cite

For GFN2-xTB (default method):

For CREST (conformer searches):

  • P. Pracht, F. Bohle, S. Grimme, Phys. Chem. Chem. Phys., 2020, 22, 7169-7192. DOI: 10.1039/C9CP06869D

See the xtb GitHub repository for other citations.