openmm-tutorial-msbs

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updates: - [github.com/nbQA-dev/nbQA: 1.7.0 → 1.8.5](https://github.com/nbQA-dev/nbQA/compare/1.7.0...1.8.5) - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0) - [github.com/kynan/nbstripout.git: 0.6.1 → 0.7.1](https://github.com/kynan/nbstripout.git/compare/0.6.1...0.7.1) - [github.com/psf/black: 23.9.1 → 24.4.2](https://github.com/psf/black/compare/23.9.1...24.4.2) - [github.com/pycqa/isort: 5.12.0 → 5.13.2](https://github.com/pycqa/isort/compare/5.12.0...5.13.2) - [github.com/asottile/pyupgrade: v3.15.0 →...

pre-commit-ci[bot]

About heating step in OpenMM

2

Thanks for the amazing tutorial! It is very helpful! I wonder why in most OpenMM protocols the temperature is directly set to the production temperature? In comparison, most Amber tutorials...

shaoqx

This comment is no longer accurate according to the referenced OpenMM issue. https://github.com/molmod/openmm-tutorial-msbs/blob/4bed3e2837e5acdca0e5d36bcbe3ed7e06eef7b9/01_first_steps/01_water.ipynb#L206

jeveki

VSC setup broken

1

Setting up the environment on VSC does not work anymore in my case. Following the [instructions](https://github.com/molmod/openmm-tutorial-msbs/blob/main/setup_vsc.md), I can no longer open Jupyter Lab. When clicking the launch button, the session...

jeveki

updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.3 → v0.6.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.3...v0.6.8)

pre-commit-ci[bot]

Bumps [numexpr](https://github.com/pydata/numexpr) from 2.8.4 to 2.8.5. Changelog Sourced from numexpr's changelog. Changes from 2.8.5 to 2.8.6 The sanitization can be turned off by default by setting an environment variable, set...

dependabot[bot]

updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.11.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.6...v0.11.7)

pre-commit-ci[bot]

It would be useful to have 'manual' installation instrictions for micromamba for people that require more flexibility in their environment (starting master thesis and PhD students).

jeveki

updates: - [github.com/astral-sh/ruff-pre-commit: v0.13.0 → v0.14.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.0...v0.14.4)

pre-commit-ci[bot]

Bumps [jupyterlab](https://github.com/jupyterlab/jupyterlab) from 4.4.4 to 4.4.8. Release notes Sourced from jupyterlab's releases. v4.4.8 4.4.8 (Full Changelog) Bugs fixed Debugger: Only send the configurationDone message once as per the DAP #17912...

dependabot[bot]