merge back the updated content

.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"
+    }
+  ]
+}

.github/workflows/build.yaml

@@ -69,7 +69,8 @@ jobs:
         run: |
           docker run -t ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:latest bash -c " \
             pip install pytest nbmake; \
-            find . -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600; "
+            which sander.MPI; \
+            find OPENMM/ -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600; "
 
       - name: Authenticate with GHCR
         if: github.event_name != 'pull_request'
@@ -100,7 +101,8 @@ jobs:
         run: |
           docker run -t ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}@${{ steps.build.outputs.digest }} bash -c " \
             pip install pytest nbmake; \
-            find . -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600; "
+            which sander.MPI; \
+            find OPENMM/ -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600; "
 
       - name: Export digest
         if: github.event_name != 'pull_request'

.gitignore

@@ -186,7 +186,7 @@ cython_debug/
 #  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
 #  and can be added to the global gitignore or merged into this file. However, if you prefer, 
 #  you could uncomment the following to ignore the entire vscode folder
-# .vscode/
+.vscode/
 
 # Ruff stuff:
 .ruff_cache/

AMBER/README.md

@@ -0,0 +1,20 @@
+# amber-md-run
+
+Tutorial on running protein-ligand simulations with the Amber MD engine.
+
+## Instructions
+
+Clone this repo then:
+
+* If you are NOT using the CBA Jupyterhub or the Docker image, first execute `run_notebook.sh` in the root directory. This will install everything required, then launch the notebook from this directory with `jupyter lab amber-md-run.ipynb`.
+* If you ARE using the CBA Jupyterhub, just open the file `amber-md-run.ipynb`.
+
+## Author
+
+@hughests
+
+## Contributors
+
+Charlie Laughton charles.laughton@nottingham.ac.uk
+
+Jas Kalayan jas.kalayan@stfc.ac.uk

AMBER/md.in

@@ -10,8 +10,8 @@ Basic MD run:
  - run at constant pressure
 
 &cntrl
-  imin = 0, nstlim = 10000, dt=0.002,
-  ntwx = 1000, ntpr = 50, ntwr = 500,
+  imin = 0, nstlim = 1000, dt=0.002,
+  ntwx = 500, ntpr = 50, ntwr = 500,
   iwrap = 1, 
   ntc = 2, ntf = 2, ntb = 2,
   ntt = 3, gamma_ln = 5, temp0 = 310.0