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I'm working on adding an example to set up and run the entire FreeSolv set (in [this branch](https://github.com/choderalab/yank-examples/tree/freesolv/examples/hydration/freesolv)), and noticed that t…
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We need to verify whether DQC can learn energies produced by itself.
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Hello - I have a scenario where I'd like to calculate orbitals and energy in a large system (let's say several molecules), then delete some molecules (both the nuclei and oribtals) and recalculate the…
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**Ketcher version** [e.g. v2.4.2].
- Indigo Toolkit Version 1.18.0-dev.4.0-g085ab345f-x86_64-linux-gnu-11.2.1
- Ketcher Version 2.17.0-rc.2 Build at 2024-01-03; 17:17:22
- Chrome Version 120.0.…
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New data base is finished. A total of 23591 molecules (few are single atom molecules will can be filtered). Need to randomly check some of the new molecules (see attached other-molecules.txt).
[othe…
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Currently in `openff-benchmark optimize execute`, execution occurs per spec in the specified season, iterating through all selected molecules. This is normally just fine, but if a user wants to re-run…
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**Describe the bug**
Updating an atom's residue-relevant metadata does not update the same data on the corresponding residue object. Editing the residue also doesn't update the atom. I'm not sure…
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Would it be possible to calculate exciton-phonon coupling in pyscf?
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I have this error in the .err file:
```
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file VS_GR_d2_290_results-2023-27-11/molecules/VS_GR_d2_290_md.tpr, VERSION 2023.2…
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I'm using the 2.3.1 GUI. I want to use "Display in Firefox" to look at the effect of changing the SVG depiction options.
When I convert two molecules from SMI to SMI, and click "Display in Firefox"…