I would like to express my sincere gratitude for your hard work and dedication to developing Avogadro2. I’ve noticed an issue when performing geometry optimization using the xtb extension within Avogadro2. As shown in the attached screenshot, the molecular structure appears to distort significantly…

Looks a bit like it decided to make a chair cyclohexane? What happens if you get XTB => Energy? For an optimized benzene, it should be something like -15.8796407 Hartree

I performed the calculation using GFN2-xTB, the resulting total energy was -14.460818 Hartree.

To clarify, this is definitely with the xtb plugin using Extensions > Semi-Empirical QM (xtb) > Optimize and not with the xtb-energy plugin?

Yes, I am using the xtb plugin. To be specific, I run Extensions > Semi-Empirical QM (xtb) > Optimize first, and after that, I execute Extensions > Semi-Empirical QM (xtb) > Energy. [pic1] Just for comparison, the following is the result of running Extensions > Semi-Empirical QM (xtb) > Energy af…

Sorry, I realized I didn’t fully answer your question in my previous message. It seems that GFN2 within the Auto Optimize tool is also not functioning correctly.

I was able to reproduce this myself on Windows, and I think I’ve identified the problem to be an xTB/conda bug, not a problem with the xTB plugin. It seems that, for some reason, the Conda version of xTB is not functioning properly on Windows ( which has been noted by others ), but the actual precomp…

That’s a little frustrating. Thanks for uncovering that. I’ll have a think about options.

I found the same problem - geometry distortion with Semi-Empirical QM (xtb) geometry optimization.

I’ve got (what should be) a solution pretty much ready, should be out in a day or two.

Avogadro Discussion

Molecular distortion during xtb optimization in Nightly 1.103.0

General Discussion Support