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TODO
- [ ] diagonalize for pertubation of degenerated eigenvalues
- [x] extend to the case when n0 has more than one site
- [ ] missing w in the calculations?
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Quick overview of tasks:
- [x] Basic connection to VMD
- [x] Loading output file
- [x] Checking for version and file type
- [x] Loading Structure
- [x] Loading Coordinate
- [x] Parsing GTO bas…
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**Summary**
Add new namespace "elements" with tables/maps and functions accessing them for a variety of mappings related to chemical elements and their properties like atomic number, atomic mass, c…
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Hi,
I am trying to overfit espaloma to a small batch from **gen2** dataset. I noticed that the reference energy **u_ref** is in large negative scale:
```
ds = esp.data.dataset.GraphDataset.load…
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I am attempting to configure the easyblock for gromacs (https://github.com/easybuilders/easybuild-easyblocks/blob/11870c2e93df143587b842cb93524f848418086c/easybuild/easyblocks/g/gromacs.py) with suppo…
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These are parameter splits I added based on my [2D k vs equilibrium value dashboard](https://github.com/ntBre/lipoma/blob/master/twod.py). The refitting files can be found [here](https://github.com/nt…
ntBre updated
8 months ago
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**MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode -1.**
**ERROR:**
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
…
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Hi all,
We found the attached compounds are challenging for force field parameterization so we would like to share those data here to 1, see if Openff could parameterize it better. 2, potentially …
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### Solution to issue cannot be found in the documentation.
- [X] I checked the documentation.
### Issue
Existing AmberTools 23 binaries (or at least `antechamber`) crash on macOS 13 where they wou…
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[eChem: A notebook exploration of quantum chemistry](https://chemrxiv.org/engage/chemrxiv/article-details/62d1764827b1e447bb3c47b1)
[AutoSolvate](https://aip.scitation.org/doi/abs/10.1063/5.0084833)
…