Xiaorui Dong
Xiaorui Dong
This is a special case where a ring flip is involved. The molecule is CC1([CH]CO)COO1.  The red rotor is the rotor being scanned, rotors in other colors are those...
**Describe the bug** I found that, when restarting a job, ARC will run freq jobs for unfinished sp jobs or composite jobs. An example is shown below:  **How to...
Force field conformer jobs of prenol, 2,3-dimethylbut-2-ene and their radicals, RO2, RO2H, OOQOOH indicates they could possess free CH3 rotors in MMFF94s. Here, I provide an example of prenol. 2D...
Details to be added...
See https://github.com/grimme-lab/xtb/issues/773. The fix (added in 2023) is merged but mctc-lib haven't had a new release since Aug 22. This makes newer xtb doesn't support Ein. XTB version should be
Haven't figured out the reason yet. Potentially related to this [issue](https://github.com/pyg-team/pytorch_geometric/issues/9077#issuecomment-2017379729). TS-EGNN includes a modified version of EGNN implementation from https://github.com/lucidrains/egnn-pytorch. Even after incorporating the new changes of PyG (changing...
The authors suggest switching to [tblite](https://github.com/tblite/tblite) instead. tblite is distributed with conda-forge's xtb. It has a python interface, tblite-python which is the replacement of xtb-python
Tested: [H].C[CH2] ; [O].C[CH2]; [H].CC; [O].CC A potential workaround: replace [H] to [Cl] and [O] to [F] during the optimization
Openbabel 3.1 has a mistake in generating radical molecules from XYZs. This influences TS-GCN notebook that uses openbabel as the backend to perceive XYZs for radicals. A temporary fix here...
Similar to https://github.com/rdkit/rdkit/issues/6208. About 3 - 20x slower according to their benchmark. This will be fixed in 2023.09 version of RDKit. Using the `[mol.GetAtomWithIdx(i) for i in range(mol.GetNumAtoms)]` as a...