Upstream sync

.github/renovate.json

@@ -0,0 +1,48 @@
+{
+  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+  "extends": [
+    "config:best-practices",
+    "helpers:pinGitHubActionDigestsToSemver"
+  ],
+  "timezone": "Europe/London",
+  "schedule": ["after 5am and before 5pm every weekday"],
+  "dependencyDashboard": true,
+  "assignees": ["jimboid"],
+  "minimumReleaseAge": "3 days",
+  "packageRules": [
+    {
+      "matchManagers": ["github-actions"],
+      "groupName": "GitHub Actions",
+      "addLabels": ["ci", "dependencies"]
+    }
+  ],
+  "customManagers": [
+    {
+      "customType": "regex",
+      "managerFilePatterns": [
+        "/(^|/)Dockerfile[^/]*$/"
+      ],
+      "matchStringsStrategy": "recursive",
+      "matchStrings": [
+        "pip3? install[\\s\\S]*?(?<packages>(?:[\\w.-]+==[\\w.-]+[\\s\\\\]*)+)",
+        "(?<depName>[\\w.-]+)==(?<currentValue>[\\w.-]+)"
+      ],
+      "datasourceTemplate": "pypi",
+      "versioningTemplate": "pep440"
+    },
+    {
+      "customType": "regex",
+      "managerFilePatterns": [
+        "/(^|/)Dockerfile[^/]*$/"
+      ],
+      "matchStringsStrategy": "recursive",
+      "matchStrings": [
+        "(?:mamba|conda) install[\\s\\S]*?(?<packages>(?:(?:[\\w-]+::)?[\\w.-]+=[\\w.-]+[\\s\\\\]*)+)",
+        "(?:(?<channel>[\\w-]+)::)?(?<depName>[\\w.-]+)=(?<currentValue>[\\w.-]+)"
+      ],
+      "datasourceTemplate": "conda",
+      "registryUrlTemplate": "https://api.anaconda.org/package/{{#if channel}}{{channel}}{{else}}conda-forge{{/if}}/",
+      "versioningTemplate": "pep440"
+    }
+  ]
+}

.gitignore

@@ -205,3 +205,16 @@ cython_debug/
 marimo/_static/
 marimo/_lsp/
 __marimo__/
+
+# Files generated by running the workshop notebooks
+notebooks/*.dcd
+notebooks_with_solutions/*.dcd
+!notebooks/trajectory_gpu.dcd
+!notebooks_with_solutions/trajectory_gpu.dcd
+notebooks*/ligand.prmtop
+notebooks*/ligand.inpcrd
+notebooks*/ligand_pointenergy.in
+notebooks*/complex.gro
+notebooks*/complex.top
+notebooks*/complex_pointenergy.mdp
+notebooks*/topology.json

README.md

@@ -29,7 +29,7 @@ Answers to most exercises are given in the [notebooks_with_solutions directory](
 
 ### Acknowledgements
 
-Most of the material for the notebook [Parameterising small molecules with OpenFF](notebooks/small_molecule_parameterisation.ipynb) was adapted from the [2023 CCPBioSim Workshop Open Force Field Sessions](https://github.com/openforcefield/ccpbiosim-2023?) created by Matt Thompson and Jeff Wagner.
+Most of the material for the notebook [Parameterising small molecules with OpenFF](notebooks/small_molecule_parameterisation.ipynb) was adapted from the [2023 CCPBioSim Workshop Open Force Field Sessions](https://github.com/openforcefield/ccpbiosim-2023?) created by Matt Thompson and Jeff Wagner, as well as the [Simulating Post-Translationally Modified Proteins with the OpenFF Rosemary Alpha Workshop](https://github.com/openforcefield/2026-virtual-workshops/blob/main/ptm/ptm-workshop.ipynb) from Ashley Mitchell.
 
 Most of the material for the notebook [Parameterisation, molecular dynamics, and basic trajectory analysis for a protein-ligand complex](notebooks/protein_ligand_complex_parameterisation_and_md.ipynb) was adapted from the OpenFF [toolkit showcase](https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/toolkit_showcase/toolkit_showcase.html) and the [ProLIF Ligand-protein MD tutorial](https://prolif.readthedocs.io/en/latest/notebooks/md-ligand-protein.html#ligand-protein-md).
 

docker/Dockerfile

@@ -9,10 +9,18 @@ USER $NB_USER
 WORKDIR $HOME
 
 # Install workshop deps
-RUN conda install -c conda-forge "openff-toolkit-examples>=0.17.0" "openff-interchange>=0.4.7" MDAnalysis prolif py3dmol openbabel -y
-
-COPY docker/fix-nglview.sh /tmp/fix-nglview.sh
-RUN bash /tmp/fix-nglview.sh
+RUN conda install -y -c conda-forge \
+    conda-forge::openff-toolkit-examples=0.19.0 \
+    conda-forge::openff-interchange=0.5.4 \
+    conda-forge::packmol=21.2.1 \
+    conda-forge::ambertools=26.0 \
+    conda-forge::MDAnalysis=2.10.0 \
+    conda-forge::prolif=2.2.1 \
+    conda-forge::py3dmol=2.5.4 \
+    conda-forge::openbabel=3.2.1
+
+#COPY docker/fix-nglview.sh /tmp/fix-nglview.sh
+#RUN bash /tmp/fix-nglview.sh
 
 # Get workshop files and move them to jovyan directory.
 COPY --chown=1000:100 . .

environment.yaml

@@ -3,8 +3,10 @@ channels:
     - conda-forge
 dependencies:
     - jupyterlab
-    - openff-toolkit-examples>=0.17.0 # New version needed for NAGL compat.
-    - openff-interchange>=0.4.7 # New version needed for NAGL compat.
+    - openff-toolkit-examples>=0.19.0 # Need at least 0.17.0 for NAGL compat.
+    - openff-interchange>=0.5.4 # Need at least 0.4.7 for NAGL compat.
+    - packmol # Needed to pack water box only
+    - ambertools # Needed for AM1-BCC charge assignment comparison only
     - MDAnalysis
     - prolif
     - py3dmol # For 3D visualization of of interactions in prolif