Avogadro Project

Screenshot showing a dialog "Geometry Optimization Parameters" with a section "Optimization Method" and "Force field" with a popup menu with a long list: AIMNet2, AIMNet-NSE, ANI-1x, ANI-2x, GAFF, GFN-FF, GFN1, GFN2, LJ, MMFF94, UFF and in the background are "Convergence Criteria" Energy convergence and Gradient convergence and Step limit: 5000 steps, with buttons Cancel and OK

Coming soon in Avogadro 2.0… 👀

Loadable energy plugins, including ML (ANI, AIMNET, MACE …) and XTB (GFN-FF, GFN1, GFN2)

Easy to add .. what models would you want to see?

Screenshot of a molecule with a dialog box labeled "Partial Charges" indicating a popup menu with items: ABCG2, AM1-BCC, EEM, EEM 20215, EEQ, EEQ-BC, EQEq, Gasteiger, MMFF94 in front of text label "Colormap" and a button labeled "OK"

Coming soon... electrostatic model plugins 👀

#openscience #compchem

Avogadro Stories (for 2.0 Release) As we finish up the 2.0 (final!) release, I’d like to feature some stories (and citations) about how Avogadro has shaped research and teaching. So if Avogadro has helped your research, please let me ...

Has @avogadro.cc helped your research? Teaching?

As we prepare Avogadro 2.0 for release this spring, I'm hoping to feature some stories (and citations).

#compchem #opensource #openscience ⚗️

Let me know:
discuss.avogadro.cc/t/avogadro-s...

Don't worry, v2.0 is still coming soon, with faster startup, an improved plugin system and improved automation capabilities

Lots more planned for 2026...

Volumetric rendering of LUMO (lowest unoccupied molecular orbital) of DyO2 molecule using Avogadro 1.103 with red and blue "clouds" representing the orbital density

Screenshot of Avogadro 1.103 with the peptide builder window open and a short oligopeptide helix in the background. The peptide builder has buttons representing different amino acids, secondary structure (alpha helix selected), phi and psi angles, and a sequence reading Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala

Screenshot of Avogadro 1.103 with a NO2 molecular orbital representing the beta-HOMO, as well as the molecular orbital window with a list of alpha and beta orbitals, orbital energy eigenvalues, and up and down arrows representing electron occupation

Screenshot of ball-and-stick representation of fmoc-protected glycine amino acid, with the fmoc protecting group highlighted in light blue after insertion with the template tool

It's 06-02, so a new release - v 1.103

Highlights include new volumetric rendering, faster orbital calculation, return of the peptide builder, new keyboard shortcuts to add functional groups and ligands, better support for open-shell orbitals, and much more...

discuss.avogadro.cc/t/avogadro-1...

Rendering of highest occupied molecular orbital (HOMO) of a conjugated molecule showing conventional orbital isosurfaces in red and blue bubbles.

Rendering of highest occupied molecular orbital (HOMO) of a conjugated molecule showing volumetric electron density in shades of red and blue clouds

Obviously a lot is going on (gestures widely)

Amid chaos, I cope by doing *something* -- anything. Lately, it's been coding for @avogadro.cc because it feels like some small change I can do myself

For *years* I've wanted to show electron density volumes .. little clouds ☁️☁️

#compchem

Avogadro Discussion Discussion about the Avogadro molecular editor

We are aiming for a release of Avogadro 2.0 on 06-Feb (06/02 😉)

If you are running into bugs or problems, please report them soon! #compchem

discuss.avogadro.cc

We just passed 3M downloads worldwide! 🎉 🎉

Thanks to all our users - it's been a great start and we look forward to more great things to come!

#chemsky #compchemsky

Dialog with text "Autosave files were found from a previous session. Would you like to recover them" and buttons "No" and "Yes"

👀

We just uploaded a video showing off the new template tool, building up triphenyl phosphine oxide.

You can easily add atoms with specific geometries, and click to add functional groups.

We include over 150 with 2D previews. Suggestions always welcome:
discuss.avogadro.cc

youtu.be/RC4NZp6nnD8

Avogadro Project Avogadro is a free open source molecular visualization and editor, designed for students and advanced researchers alike. Used in computational chemistry, molecular modeling, chemistry education, bioin...

We've been starting up some tutorial videos on Avogadro2 🎬🍿
www.youtube.com/@AvogadroPro...

What topics would you like us to cover? Let us know over at discuss.avogadro.cc

#compchem #chemsky

It's 10-23 day! So we decided to make a new release:
- AutoOptimize Tool 🎉
- New charts and spectra
- Easier geometry constraints, including for ORCA input
- Plenty of bug fixes and tweaks

discuss.avogadro.cc/t/avogadro-1...

It's 10-23 day! So we decided to make a new release:
- AutoOptimize Tool 🎉
- New charts and spectra
- Easier geometry constraints, including for ORCA input
- Plenty of bug fixes and tweaks

discuss.avogadro.cc/t/avogadro-1...

Avogadro2 - Free download and install on Windows | Microsoft Store Avogadro is a molecular editor and visualization tool, designed for students and researchers alike. Used in computational chemistry, molecular modeling, chemistry education, bioinformatics, materials ...

Do you use Windows? We're now on the Windows app store:

We will now offer signed MSIX packages with releases, in addition to the traditional installer.

apps.microsoft.com/detail/9n21v...

Let us know how it works at discuss.avogadro.cc

Tested out some water clusters during lunch.
- MMFF94 has point charges and hydrogen bonds
- UFF does not (so water molecules push apart)

At some point I'll add some simple dynamics…

#compchem #compchemsky

Screenshot of Avogadro2 using the interactive AutoOptimize tool to minimize a molecule (n-pentane) using the UFF force field. Text reads UFF ΔE = -229.80 kcal/mol

If you've been wondering about the status of the AutoOptimize interactive optimization in Avogadro2 - coming later this month 👀

Great! Let us know at discuss.avogadro.cc if there are particular features you'd like to see.

Dialog titled "Vibrational Spectra" showing the computed infrared spectra of caffeine with two plots, one in black labeled "smoothed" and one in red labeled "raw"

👀

Coming soon...

The atoms have essentially infinite resolution, but the real-time shadows / ambient occlusion does not. The latter looks better on high-resolution screens.

Having reflectivity as an option seems useful - please post a feature request

Might depend on your computer and rendering options. We offload a variety of things to the GPU. Some users have asked for real-time shadows, etc. to be turned off by default (View => Rendering… options)

We've got a new release 1.101, which should particularly fix some bugs with Windows and Mac, and of course a variety of new features.

Highlights include support for constraints for geometry optimizations, tweaking bond lengths when changing elements, and more...

discuss.avogadro.cc/t/avogadro-1...

Thanks!

A few tips:
- If you use Avogadro 1.100 or later, you'll get the list of orbitals you mentioned
- The resolution of the exported graphic currently depends on your screen

If you (or anyone else) experiences bugs or has suggestions, please let us know at discuss.avogadro.cc

Thanks to a suggestion from a user, we've been working on some tweaks to the draw tool...

Now you can click on a hydrogen atom to change the element and the bond will grow longer or shrink as needed

Coming soon to the next release (or in a nightly build)

To be clear, volumetric rendering of molecular orbitals, electron density, etc. will soon be available:

discuss.avogadro.cc/t/volumetric...

Colors are configurable...

Volumetric "cloud" rendering of highest occupied molecular orbital (HOMO) of benzene in Avogadro 2

Volumetric "cloud" rendering of highest occupied molecular orbital (HOMO) of caffeine in Avogadro 2

What's this? 🤔

Working on something new... #opensource #compchem

Molecular rendering of a tetrapeptide with translucent van der Waals spheres and balls-and-sticks backbone

Rendering of C60 fullerene with highest-occupied molecular orbital (HOMO) in translucent blue and red surfaces with a window listing all molecular orbitals, energies and rendering status

Molecular properties window, listing molecule name (C60-Ih)[5,6]fullerene or C60 fullerene, molecular mass, chemical formula, number of atoms, number of bonds, net charge, net spin multiplicity, dipole moment (0.0), HOMO and LUMO orbital energies in eV

We're starting off 2025 with a new release - 1.100

Highlights include new blur and fog rendering, faster orbital surfaces, return of the MO table, translucent balls-and-sticks, conformer properties, an improved molecular properties window, and more...

discuss.avogadro.cc/t/avogadro-1...

Thanks for the update - glad to know it's working for you!

Avogadro Discussion Discussion about the Avogadro molecular editor

We're finishing up a new release, but trying to track down some bugs 🪲 #compchem

Some Windows users report Avogadro 1.99 won't even launch. If this is you and you're willing to test a new build, please let us know at discuss.avogadro.cc

No problem - please let us know about the current nightly builds when you have a chance at discuss.avogadro.cc

Thanks

2024 Year-In-Review While it’s not strictly the end of 2024, I wanted to draft this early. Obviously a highlight is the release of 1.99 in time for Ubuntu LTS (24.04) … a summer of great coding / rendering, leading to t...

I wrote up a 2024 Year in Review for @avogadro.cc 🧪⚗️ #opensource #chemsky

In short, the community is amazing. Significant translations into 17 languages including 🇭🇷🇫🇷🇭🇺🇰🇷🇷🇴🇪🇸Tamil, 🇺🇦🇨🇳🇬🇪🇩🇪🇯🇵🇵🇹🇧🇷🇷🇸🇹🇷

.. and of course dozens of features and bug fixes discuss.avogadro.cc/t/2024-year-...