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Reposted by Avogadro Project

Geoff Hutchison @geoffhutchison.net · 1d

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 · 2d

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 · 10d

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 · 11d

👀

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 · 22d

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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Avogadro Project @avogadro.cc · 22d

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)

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Avogadro Project @avogadro.cc · 22d

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...

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Avogadro Project @avogadro.cc · 22d

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

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Avogadro Project @avogadro.cc · Jun 2

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)

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Avogadro Project @avogadro.cc · Mar 25

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

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

Colors are configurable...

Avogadro Project @avogadro.cc · Mar 23

What's this? 🤔

Working on something new... #opensource #compchem

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

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Avogadro Project @avogadro.cc · Mar 23

What's this? 🤔

Working on something new... #opensource #compchem

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Avogadro Project @avogadro.cc · Jan 22

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...

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

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Avogadro Project @avogadro.cc · Jan 6

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

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Reposted by Avogadro Project

Avogadro Project @avogadro.cc · Dec 27

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

Avogadro Discussion

Discussion about the Avogadro molecular editor

discuss.avogadro.cc

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Avogadro Project @avogadro.cc · Jan 5

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

Thanks

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Reposted by Avogadro Project

Geoff Hutchison @geoffhutchison.net · Dec 30

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-...

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...

discuss.avogadro.cc

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Avogadro Project @avogadro.cc · Dec 28

Please open a new thread - there’s a new nightly build that should provide more details.

Is there a previous version that worked? Thanks!

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Avogadro Project @avogadro.cc · Dec 27

In the meantime, enjoy some nice screenshots of work-in-progress... #compchem

Screenshot of Avogadro 1.100 showing molecular orbital list and lowest unoccupied molecular orbital (LUMO) of benzene

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Avogadro Project @avogadro.cc · Dec 27

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

Avogadro Discussion

Discussion about the Avogadro molecular editor

discuss.avogadro.cc

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Avogadro Project @avogadro.cc · Dec 2

We've got a "Cyber Monday" special discount too!

Download a nightly build today 🧪 #chemsky

Avogadro Project @avogadro.cc · Nov 30

In honor of Black Friday in the US, we've got a special discount! Use "Open Source" and you can get Avogadro 1.99 for free!

Wait, you *never* need a discount code? It's #opensource and #openscience

Visit two.avogadro.cc and discuss.avogadro.cc to see what we've been doing for Avogadro v2.

Screenshot from Avogadro showing a C60 buckminsterfullerene cage with a translucent sodium atom inside

Screenshot of a zirconacene catalyst with zirconium atom marked as "Zr" surrounded by a translucent van der Waals sphere illustrating the size of the metal atom and its interaction with the ligands

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Avogadro Project @avogadro.cc · Nov 30

In honor of Black Friday in the US, we've got a special discount! Use "Open Source" and you can get Avogadro 1.99 for free!

Wait, you *never* need a discount code? It's #opensource and #openscience

Visit two.avogadro.cc and discuss.avogadro.cc to see what we've been doing for Avogadro v2.

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Avogadro Project @avogadro.cc · Feb 11

We're back with a new release! 🎉

Highlights include improved force field optimizations, faster surfaces & orbitals, vibration spectra plots, and new tool icons, plus dozens of bug fixes, features, and new script plugins

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

Molecular depiction of caffeine including solvent accessible surface

Calculated vibrational spectra of caffeine

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Reposted by Avogadro Project

Geoff Hutchison @geoffhutchison.net · Nov 27

As someone who went to grad school as an inorganic chemist, it gives me some pleasure to finally have a free tool to click-click-click assemble iron bipyridine complexes or Ziegler-Natta catalyst models in @avogadro.cc in about the same time it takes to build an organic compound. #chemsky 🧪

Image of trisbipyridine iron(II) complex

Image of zirconium Ziegler-Natta catalyst with Zr atom bonded to two eta5-cyclopentadyenyl ligands, an eta-2 ethylene ligand, and a methyl group

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Avogadro Project @avogadro.cc · Nov 3

We're happy to announce v1.98, the latest beta of Avogadro2, including piles of new features and bug fixes, including support for 3Dconnexion devices on Windows and Mac #compchem

Lots more - see: discuss.avogadro.cc/t/avogadro-1...

Image of gold nanoparticle showing real-time shadows on atom spheres

Image of molecule showing dashed lines between close contacts - non-bonded interactions

Image of DNA base pair showing dashed blue lines representing hydrogen bonds

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