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Avogadro Project

@avogadro.cc
366 followers 33 following 58 posts

Advanced molecule editor and visualizer Building the next generation of molecular and materials visualization and editing tools avogadro.cc discuss.avogadro.cc

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Avogadro Project @avogadro.cc · 01/10/2026
What's this? Avogadro2 in a web browser?! #compchem #opensource #prototype
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Avogadro Project @avogadro.cc · 24/09/2026
Hmm, what's this? discuss.avogadro.cc/t/need-feedb...
Screenshot indicating two water molecules. Oxygen atoms are indicated with #1 and #4 symbols, with a panel on the left side indicating measurements, such as Distance 1-2 0.958 A, Distance 2-3 2.000 A, etc. allowing editing to change the distances and angles...
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Avogadro Project @avogadro.cc · 14/09/2026
Looks like a 60 / 40 split in favor of "Z-Matrix Editor" so we'll try to jam "internal coordinates" in there somehow.
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Avogadro Project @avogadro.cc · 11/09/2026
Hmm. ⚔️
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Avogadro Project @avogadro.cc · 11/09/2026
Well, it's a 3D editor.. 😀 There are some interesting ideas to get Avogadro2 working on the web. Need a bit more tooling, but probably sometime next spring. The big trick is full v3000 support, e.g. dative, haptic bonds, etc. but suggestions and help are definitely welcome!
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Avogadro Project @avogadro.cc · 11/09/2026
Yes, that's the general idea. If you decide you want the distance to go from atom 4 instead of atom 2, it'll figure it out. We're just trying to gauge how many people use the two terms. You should be able to test it out in the continuous builds now avogadro.cc/install/
avogadro.cc
Install — Avogadro 2.0.0 documentation
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Avogadro Project @avogadro.cc · 11/09/2026
Several people said it was the only reason they still used Molden?
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Avogadro Project @avogadro.cc · 11/09/2026
We've been working on an internal-coordinate / z-matrix editor. How should we name it? #compchem (Keep in mind we need to translate into multiple languages) 1️⃣ Z-Matrix Editor 2️⃣ Internal Coordinate Editor 📊 Show results
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Avogadro Project @avogadro.cc · 11/09/2026
We've been working on an internal-coordinate / z-matrix editor. How should we name it? #compchem (Keep in mind we need to translate into multiple languages) 1️⃣ Z-Matrix Editor 2️⃣ Internal Coordinate Editor 📊 Show results
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Reposted by Avogadro Project
Geoff Hutchison @geoffhutchison.net · 29/08/2026
A few weeks ago, I posted for the 2026 Avogadro Community Feedback Survey. Over 50 people responded, and several wrote multi-paragraph responses! I posted a summary to the forum and I want to include a few notes for #compchem discuss.avogadro.cc/t/avogadro-2...
discuss.avogadro.cc
Avogadro 2026 Survey Results
A few weeks ago, I posted the 2026 Community Feedback Survey - and I’d like to start doing this annually. Thank you to the 49 50 of you who filled out the development survey. Several people wrote…
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Avogadro Project @avogadro.cc · 08/08/2026
Do you use Avogadro? We'd like some feedback: No personal information is required - just a few minutes #compchem #chemsky forms.gle/FqNo8xe9KMPH...
forms.gle
Avogadro Community Feedback
Now that we've released Avogadro 2.0, we'd like to gain feedback and information on the user community -- how it's used, what you use it for, and how you heard about it to guide future development. T...
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Avogadro Project @avogadro.cc · 08/08/2026
Do you use Avogadro? We'd like some feedback: No personal information is required - just a few minutes #compchem #chemsky forms.gle/FqNo8xe9KMPH...
forms.gle
Avogadro Community Feedback
Now that we've released Avogadro 2.0, we'd like to gain feedback and information on the user community -- how it's used, what you use it for, and how you heard about it to guide future development. T...
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Avogadro Project @avogadro.cc · 07/08/2026
Do you have an example use case or tool you use a lot?
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Avogadro Project @avogadro.cc · 06/08/2026
Avogadro now has over 25 Python plugins for: - input generation for common programs - partial charges and electrostatics - reading and writing file formats through cclib - forcefields and ML potentials - building and analysis commands What are some tools you'd like to see? #compchem
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Avogadro Project @avogadro.cc · 22/05/2026
We're still working... @geoffhutchison.net reports on new speedups coming in v2.1 scheduled for June 02 (6/02 in the states 😉) - 20-25x faster orbital and density calculations - 6-8x faster geometry optimizations using an adaptive FIRE+L-BFGS method discuss.avogadro.cc/t/may-2026-d... #compchem
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Avogadro Project @avogadro.cc · 08/04/2026
Shortcuts can all be found at avogadro.cc/docs/tools/k... As always, suggestions welcome!
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Avogadro Project @avogadro.cc · 08/04/2026
Thanks! If you'd like to write up a summary of an activity, we'd welcome more contributions at avogadro.cc/teach/ Just let us know on the forum discuss.avogadro.cc
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Avogadro Project @avogadro.cc · 07/04/2026
And if you'd like to help with translation, please check out avogadro.cc/contrib/tran...
avogadro.cc
Translations — Avogadro 2.0.0 documentation
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Avogadro Project @avogadro.cc · 07/04/2026
One week of Avogadro 2.0 highlights - and we're just getting started… Download: avogadro.cc/install/ Join the community: discuss.avogadro.cc Thanks to everyone who helped make this release happen. Open science is a team effort! Got ideas on where to go next? 🧪 ⚗️ #opensource #openscience #compchem
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Avogadro Project @avogadro.cc · 06/04/2026
Avogadro 2.0 isn't just a viewer and editor — it's an extensible platform for chemistry A plugin system lets you add ML & electrostatic models, new builders and tools. Already over 20 available… Build the tools you need: avogadro.cc/develop/plug... #avogadro #openscience #compchem #opensource
Screenshot of "Manage Plugins" window in Avogadro2, including over 20 plugins. A table shows several plugins including generators, RDKit, cclib, build-ase, xtb, aimnet2, genice2, TurtleMol, multicharge, antechamber, chiraltube, etc. with a README on the right hand side and buttons to search, install from a local directory, remove selected, and install / update selectedScreenshot of an example plugin for Chiraltube, indicating n, m values, number of repeats, and material, with MoS2 selected and the generated nanotube in the background with yellow spheres for sulfur atoms and turquoise spheres for Mo atomsScreenshot of ORCA input generator, showing Basic, SCF, Basis, and Electronic Property tabs, and input file text.
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Avogadro Project @avogadro.cc · 05/04/2026
Also, not sure if MMFF94 (used for this) is the best choice for liquid water. On the other hand, it's useful to switch between say UFF (which lacks electrostatics and h-bonding terms) and MMFF94. At the moment, we don't yet have support for various water models (TIP3P, TIP4P, SPC, etc.)
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Avogadro Project @avogadro.cc · 05/04/2026
Are these different?
Meme: Corporate needs you to find the differences between this picture and this picture. Text on the left reads "Avogadro 2.0" text on the right reads "Avogadro2 2.0"
Bottom panel depicts Pam from The Office saying "They're the same picture."
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Avogadro Project @avogadro.cc · 05/04/2026
Yes, this didn't start from an equilibrated water box, so the density is wrong. If you've got some good suggestions for initial starting points (e.g., for teaching purposes), they'd be greatly appreciated!
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Avogadro Project @avogadro.cc · 05/04/2026
Sometimes you just want to see a molecule move. Run a quick MD simulation without leaving Avogadro — no scripts, no setup. The new auto-optimize tool includes a dynamics mode. Watch it move in real time. Great for teaching. Great for intuition. Just fun to watch. #openscience #compchem #opensource
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Avogadro Project @avogadro.cc · 04/04/2026
Visualize molecular orbitals and electron density easily with Avogadro 2.0. Volumetric rendering of orbitals, plus van der Waals, solvent-accessible and solvent-excluded surfaces for biomolecular work. See the chemistry, not just the atoms. #compchem #openscience #opensource
Volumetric rendering of the highest occupied molecular orbital (HOMO) of pentacene. Yellow and blue indicate opposite phases of the wavefunction, with color intensity indicating the magnitude of the wavefunctionVan der Waals molecular surface of coronene, with overlaid electrostatic potential map: red = more negative charge, blue = more positive chargeRendering of the highest occupied molecular orbital (HOMO) of pyrazineRendering of a graphene supercell with solvent-accessible surface (green) indicating a defect site with a hydrogen molecule and overlay of electrostatic potential (blue = more positive, red = more negative)
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Avogadro Project @avogadro.cc · 03/04/2026
Inorganic and organometallic chemists — Avogadro 2.0 is for you... A new template tool lets you build octahedral, tetrahedral, and other complexes in seconds. Click to add functional groups. Avogadro also detects symmetry and displays symmetry elements #compchem #openscience #opensource
Rendering of Ziegler–Natta zirconium catalyst with blue-green translucent sphere representing the Zr atom, and ball-and-stick rendering of cyclopentadienyl (Cp) rings and methyl groupScreenshot of Avogadro 2 template tool, indicating a tab for Element: Formal Charge: and the options for Coordination selected, with options 1: Linear, 2: Linear, 3: Trigonal Planar, 4: Tetrahedral, 4: Square Planar, 5: Trigonal Bipyramidal, 5: Square Pyramidal, 6: Octahedral, 6: Trigonal Prism, 7: Pentagonal Bipyramidal, 8: Square AntiprismBall and stick rendering of chlorophyll c2 molecule with larger green sphere representing the Mg(II) ionScreenshot of symmetric (D5d) ferrocene with rotation axes illustrated as red cylinders. Orange sphere is an iron atom, and grey-white cylinders indicate the cyclopentadienyl ligands. Dialog text indicates D5d symmetry, tabs for "Molecule", "Operations", "Subgroups" with operations active, indicating a table of symmetry elements, classes, and element. At the bottom of the dialog is Tolerance: Normal and a button "Detect Symmetry"
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Avogadro Project @avogadro.cc · 02/04/2026
Avogadro 2.0's rendering was rebuilt for modern GPUs. Smooth even with tens of thousands of atoms. Real-time shadows and ambient occlusion give depth and clarity — and a new layer system lets you hide solvent, toggle styles, and focus on what matters. #opensource #openscience #compchem
Visualization of the COVID spike protein 6vxx with real-time shadows in Avogadro2 to give depth effects. All hydrogen atoms are hidden. Grey spheres are carbon atoms, red spheres are oxygen, blue spheres are nitrogen, and yellow spheres are sulfur atoms.Screenshot from Avogadro showing a C₆₀ buckminsterfullerene cage with a translucent purple sodium atom insideScreen rendering of a zeolite supercell showing shadows and depth blurring. Brown spheres are silicon atoms and red spheres are oxygen atomsRendering of a protein surrounded by a solvation sphere of water in wireframe view (using red-white lines to indicate the water molecules)
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Avogadro Project @avogadro.cc · 01/04/2026
No fooling, Avogadro 2.0.0 is finally here! Rebuilt from the ground up: fast modern rendering, improved stability, designed for the next generation of molecular, biomolecule, and materials research & education. 🧪 ⚗️ avogadro.cc/install/ discuss.avogadro.cc #opensource #openscience #compchem
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Avogadro Project @avogadro.cc · 30/03/2026
Something big is coming on 1 April – and no, it's not a joke. 🧪 ⚗️ #opensource #openscience #compchem
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Avogadro Project @avogadro.cc · 30/03/2026
Something big is coming on 1 April – and no, it's not a joke. 🧪 ⚗️ #opensource #openscience #compchem
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Avogadro Project @avogadro.cc · 14/03/2026
Avogadro 2.0 drops April 1st — and no, that's not a joke! 🧪⚗️ Now's the perfect time to help improve translations before release. Every language matters for chemistry worldwide. #opensource #openscience hosted.weblate.org/engage/avoga...
hosted.weblate.org
Making sure you're not a bot!
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Avogadro Project @avogadro.cc · 10/03/2026
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 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
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Avogadro Project @avogadro.cc · 09/03/2026
Coming soon... electrostatic model plugins 👀 #openscience #compchem
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"
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Geoff Hutchison @geoffhutchison.net · 22/02/2026
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...
discuss.avogadro.cc
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 ...
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Avogadro Project @avogadro.cc · 06/02/2026
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...
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Avogadro Project @avogadro.cc · 06/02/2026
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...
Volumetric rendering of LUMO (lowest unoccupied molecular orbital) of DyO2 molecule using Avogadro 1.103 with red and blue "clouds" representing the orbital densityScreenshot 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-AlaScreenshot 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 occupationScreenshot 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
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Geoff Hutchison @geoffhutchison.net · 30/01/2026
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
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
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Avogadro Project @avogadro.cc · 20/01/2026
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
discuss.avogadro.cc
Avogadro Discussion
Discussion about the Avogadro molecular editor
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Avogadro Project @avogadro.cc · 18/11/2025
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
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Avogadro Project @avogadro.cc · 13/11/2025
👀
Dialog with text "Autosave files were found from a previous session. Would you like to recover them" and buttons "No" and "Yes"
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Avogadro Project @avogadro.cc · 08/11/2025
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
youtu.be
Building Molecules with Templates
YouTube video by Avogadro Project
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Avogadro Project @avogadro.cc · 31/10/2025
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
youtube.com
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...
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Reposted by Avogadro Project
Avogadro Project @avogadro.cc · 23/10/2025
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...
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Avogadro Project @avogadro.cc · 23/10/2025
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...
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Avogadro Project @avogadro.cc · 14/10/2025
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
apps.microsoft.com
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 ...
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Geoff Hutchison @geoffhutchison.net · 06/10/2025
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
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Avogadro Project @avogadro.cc · 06/10/2025
If you've been wondering about the status of the AutoOptimize interactive optimization in Avogadro2 - coming later this month 👀
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
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Avogadro Project @avogadro.cc · 27/09/2025
Great! Let us know at discuss.avogadro.cc if there are particular features you'd like to see.
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Avogadro Project @avogadro.cc · 27/09/2025
👀 Coming soon...
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"
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Avogadro Project @avogadro.cc · 15/09/2025
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
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