Erik Poppleton

[BUG]: Cmake cannot find Python include directories for Python 3.11 on MacOS

6

### Required prerequisites - [X] Make sure you've read the [documentation](https://pybind11.readthedocs.io). Your issue may be addressed there. - [X] Search the [issue tracker](https://github.com/pybind/pybind11/issues) and [Discussions](https:/pybind/pybind11/discussions) to verify that this hasn't...

setup.py ignoring library search environment variables.

2

In the installation instructions it says: > Environment variables: > PREFIX_PATH Colon-delimited list of paths to search for headers and > libraries, e.g. $HOME/mmtf-cpp:$HOME/msgpack-c:/opt/local > CXX C++ compiler command >...

[BUG] Relaxation of DNA structures behaves differently between recent oxDNA versions and the old one on oxServe

6

**Describe the bug** When pulling structures into desired starting configurations using mutual traps, the version of oxDNA running on the `oxServe` plugin of oxView is significantly more stable than the...

If you use `api.toggleBaseColors()` and then select and deselect a nucleotide, its color reverts to the usual color scheme rather than grey. Presumably this is because we wrote the update...

Topology and configuration file missmatch handling

3

If the .dat and .top files are missmatched, the correct error is thrown, but the page must be refreshed before files can be dropped again. This should clear the variables...

**What is the topic of your question**: Usage / Documentation, maybe Bug **Add your question below**: When I run the LyPyphilic `lateral_diffusion.MSD` module on simulations of Amber Lipid21 lipids in...