The trunk version of the Avogadro documentation is available at http://avogadro.cc/api/dev/.
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This page is a guide for newcomers to the project. It should gain some insight on how the project has been designed code-wise and save you time in the long r...
These instructions are to allow users to build Avogadro from the very latest code. Be aware that Avogadro may fail to build or work properly at any given tim...
These instructions are intended to help users and contributors build Avogadro from the latest code. Be aware that Avogadro may fail to build or work properly...
Avogadro has a very open and active development community. Currently there are more than 10 active developers and other various contributers.
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Avogadro started with a single idea. All great editors are improved by plugins.
The following are a set of links and bookmarks for developers on a range of useful topics. This includes galleries of example molecular rendering programs,
This page contains some ideas about future refactorization of libavogadro. They may seriously break ABI (and possibly API), and should be discussed
Create a draft of the release notes on the wiki. Grab the latest i18n files from Launchpad translations. Make sure to update CMakeLists.txt and Doxyfi...
When in doubt about standards, consider the policies which KDE has set (see [\
The upcoming development series 1.1.x will be a series of unstable/beta releases, leading up to the 1.2.0 release. This process will be similar to the 0.9.x ...
In December 2008 Avogadro moved its version control system over to Git, hosted at GitHub. Git is quite different to traditional, centralized version control ...
Build up a crystal surface, e.g., Pt <111> for a defined Miller Plane.
A walk-through on creating a unit cell (of a polymer) using Avogadro and the Align tool. This specific example uses Gaussian, but translation vectors for oth...
Calculation results often specify all atoms and translation vectors, but not the space group. Here we see how to perceive the space group from a set of cryst...
Beyond building a crystal surface, new features in Avogadro make it easy to consider molecule-surface interactions. The lesson picks up at the end of the “Bu...
Some simulations use “supercells” – larger periodic boundary systems than the primitive unit cell. Here is a walk-through on reducing a large supercell to th...
Avogadro 1.1 allows you to adjust the volume or spacing of a unit cell.
Once a crystal surface has been built, the Super Cell Builder can expand atoms within a space group, replicate the unit cell, and perform simple bonding.
A walkthrough on how to create a custom peptide model in Avogadro.
Avogadro 1.1 includes a new nanotube builder, based on the well-known TubeGen code and website from the Doren group at U. Delaware. (http://turin.nss.udel.ed...
Avogadro now has a builder for nucleic acid sequences and this walk-through will show you how to use it.
SMILES (Simplified molecular-input line-entry system) allows you to build molecules through a string of text. If you have a SMILES string (e.g., copied from ...
You can read PDB files that you download yourself from http://www.rcsb.org/ or access the PDB code yourself.
Select the “File” menu.
Avogadro includes over 300 common molecules and molecular fragments to make building larger structures easy.
Coloring various parts of a molecule can provide a more visually stimulating way to display qualitative information.
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Avogadro has a new interface to the open source solid-state code ABINIT, provided by one of the ABINIT developers, Prof. Matthieu Verstraete
Prepare initial geometry
Molecules are built and edited with the draw tool.
Avogadro is a “molecular editor,” designed to be easy to use to construct and view molecules and materials in 3D. It runs on Windows, Linux, and Mac.
The selection tool is also a useful feature to master when beginning to learn Avogadro. Generally, the selection tool allows for the individual selection of ...
Avogadro: Molecular Editor and Visualization
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How to search for low-energy conformations
Avogadro allows for the optimization of an object, with respect to a variable(s). Below is one example of how constraints can be applied while optimizing a m...
Avogadro comes equipped with multiple different force fields. Below is general information regarding the force fields to help you select the best optimizatio...
The align tool rotates, and translates a molecule(s) into a specific reference frame.
The Auto Optimize tool continuously optimizes molecular geometry through molecular mechanics. This tool provides an interactive interface, allowing you to ma...
The auto rotate tool allows for the continuous rotation of a molecule.
The Bond-Centric Manipulate tool alters angles, bonds, and torsions of a molecule.
1. Creating a Molecule
The manipulate tool allows you to move atoms and selected fragments.
The measure tool determines bond lengths, angles, and dihedrals.
The navigation tool is used to pan, rotate, and scale the view of a molecule.
The selection tool allows the indiviual selection of atoms, bonds, or fragments.
Avogadro 1.1 and later includes support for naming compounds using the NIH Chemical Resolver system and the PubChem database.
Avogadro now includes support for the QTAIM analysis developed by Prof. Richard Bader and his group. This technique allows Avogadro to determine bond connect...
The electrostatic potential maps help to visualize charge distribution, and other charge related properties of molecules.
This feature requires a “checkpoint” or “formatted checkpoint” from quantum chemistry codes
This tutorial covers plotting vibrational spectra, but other types of spectra are possible with the output files from quantum chemical programs
This feature allows visualizing vibrations from a “frequency” calculation with quantum chemistry codes (e.g., Gaussian, Q-Chem, etc.)
The latest and greatest release of Avogadro is Avogadro 1.2.0 as of 15 June, 2016, and release notes are available.
Avogadro version 0.1.0 was released on May 18, 2007.
Avogadro version 0.2.0 was released on October 23, 2007.
Avogadro version 0.6.0 was released on February 29, 2008.
Avogadro version 0.6.1 was released on March 8, 2008.
Avogadro version 0.8.0 was released on May 19, 2008.
Avogadro version 0.8.1 was released on 7 June 2008.
Avogadro 0.9.0 was released on 12 January 2009. This is the first of our final beta series before Avogadro 1.0.0 is released. Please help us by providing fee...
Avogadro 0.9.1 was released on 16 February 2009. This is the second of our final beta series before Avogadro 1.0.0 is released. Please help us by providing f...
Avogadro 0.9.2 was released on 1 March 2009. This is the third of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedba...
Avogadro 0.9.3 was released on 1 April 2009. This is the fourth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedb...
Avogadro 0.9.4 was released on 2 May 2009. This is the fifth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedback...
Avogadro 0.9.5 was released on 2 June 2009. This is the sixth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedbac...
Avogadro 0.9.6 was released on 5 June 2009. This is the seventh of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedb...
Avogadro 0.9.7 was released on 18 July 2009. This is the eighth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedb...
Avogadro 0.9.8 was released on 9 September 2009. This is the ninth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing fe...
Avogadro 0.9.8 was released on 17 October 2009. This is the tenth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing fee...
Avogadro 1.0.0 was released on 23 October 2009. In the US, this was announced at 6:02 10/23, or “Mole Day”.
Avogadro 1.0.1 was released on 28 April 2010.
Avogadro 1.0.2 was released on 22 April 2011.
Avogadro 1.0.3 was released on 25 April 2011. It contains a single fix for building translations.
Avogadro 1.1.0 was released on September 12, 2012.
Avogadro 1.1.1 was released on December 11, 2013.
Avogadro 1.2.0 was released on June 15, 2016.
Investigate the stability of alkene isomers due to steric interactions.
Investigate atom geometries using VSEPR rules.
Investigate polar intermolecular interactions using HCN.
Investigate the intermolecular interactions of solid hydrogen.
Investigate the hydrogen molecule and bond length using different force fields.
Investigate the stability of reactions using Markovnikov’s rule.
Illustrate the geometry and bond lengths in sp3, sp2 and sp hybridized carbons.
Investigate the geometry of water and hydrogen bonding between molecules.
Investigate the pH-dependent protonation of amino acids.
Investigate steric interactions in cyclohexane derivatives.