David L. Mobley
David L. Mobley
Several notebooks do trajectory visualization with `nglview`; it would be helpful to migrate those to something which will work on Colab. The most important seem to be: - MD sandbox...
- The ligand-based design lecture and assignment have some inconsistencies and the code in the lecture is more helpful than the example code in the assignment, students report - Check...
The visualization lecture added a couple very large files (Keynote files) which have to managed with git-lfs. A better procedure would be to just link to them (hosted elsewhere) and...
The notebooks and worked examples for lectures need updating, particularly, these cases: - [x] Python, Linux, and vi(m) - [x] 3D structure and shape methods (#25 ) - [x] **Molecular...
Currently, I do not have Jupyter notebooks for the following lectures, so I will need to create them (potentially from the slides), ideally also creating activities to try at the...
- Improve images/make sure all have suitable credit/attribution - Migrate to Jupyter notebook? Unsure if content lends itself to that, but would make for greater portability/easier updates.
See https://github.com/openforcefield/openforcefield/issues/252
Probably want to cross check against the Netherlands eScience book on GitHub which covers a lot of ground -- https://github.com/nlesc/guide and https://guide.esciencecenter.nl/index.html -- recommended by Daniel Smith.
I was running a super short minimization/simulation and wanted to output a PDB of the OpenFF Topology to check that it had worked properly. However, we have a way to...
In https://github.com/openforcefield/openforcefield/issues/440, we've highlighted several bugs which can occur converting a SMIRNOFF system to AMBER/GROMACS format via ParmEd, including: - incorrect 1-4 scale factors - missing atom identifiers - missing...