Benjamin Ye

Hello! I am trying to read a multi-frame OpenMM-generated PDB trajectory file using `mdtraj.load_pdb(...)`, but I am getting --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /mnt/z/research/dilution/scripts/npt_analysis.ipynb Cell 5' in ()...

Incorrect "show/hide code cell output" background in dark mode

2

### Describe the bug **context** When dark mode is toggled, the "show/hide code cell output" button's text is updated to a light color, but the background stays light, making the...

Cannot load LAMMPS NetCDF trajectory files due to "header issue" in scipy.io.netcdf_file

5

## Expected behavior ## I have run a LAMMPS simulation of a simple electrolyte–solvent systems confined between two planar dielectric electrodes. During the simulation, the topology is written to LAMMPS...

Unexpected font/styling in newly rendered documentation after updating sphinx-book-theme and pydata-sphinx-theme

1

### Describe the bug **context** Hello! I've been using the Sphinx book theme for my personal project's documentation because I like the simplistic styling. However, the HTML version that I...

Minim 1.0.0 release

3

There are a few ambitious overhauls I'd like to do before the 1.0.0 release of Minim: **General** - [x] Update documentation to have consistency between the different submodules, with the...

Thanks so much to everyone who has showed interest in and/or used Minim. I never thought it would receive this much attention! After all, this is just a personal project...