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Fixes for steered MD tutorial and update to RBFE tutorial #33

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Fixes for steered MD tutorial and update to RBFE tutorial #33

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d5fd254
Updates RBFE notebook to support cinnabar 0.4.1
mb2055 Feb 21, 2025
fdc42f5
Update README to new cinnabar version
mb2055 Feb 21, 2025
b142b50
Updates CollectiveVariable.RMSD to new API
mb2055 Feb 21, 2025
9b59d85
Updates to be consistent with older versions.
mb2055 Feb 24, 2025
7466e20
Adds link to snakemake workflow to RBFE setup tutorial
mb2055 Oct 3, 2025
036ff34
Updates get_tutorial links to new location, and alters the steered md…
mb2055 Oct 10, 2025
290da5e
Post-testing changes, including slight update to node filepaths and u…
mb2055 Oct 22, 2025
4a1d0da
Blacken node running notebook
mb2055 Oct 22, 2025
7433e58
Update python version in README
mb2055 Oct 22, 2025
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22 changes: 17 additions & 5 deletions 01_introduction/05_running_nodes.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,7 @@
"outputs": [],
"source": [
"from get_tutorial import download\n",
"\n",
"download()\n",
"!ls inputs/ala*"
]
Expand Down Expand Up @@ -219,7 +220,12 @@
"metadata": {},
"outputs": [],
"source": [
"input = {\"files\": [\"inputs/ala.crd\", \"inputs/ala.top\"], \"steps\": 1000}"
"import os\n",
"\n",
"input = {\n",
" \"files\": [os.path.abspath(\"inputs/ala.crd\"), os.path.abspath(\"inputs/ala.top\")],\n",
" \"steps\": 1000,\n",
"}"
]
},
{
Expand All @@ -235,7 +241,7 @@
"metadata": {},
"outputs": [],
"source": [
"output = BSS.Node.run(\"minimise\", input)"
"output = BSS.Node.run(\"minimise\", input, work_dir=\"TEST\")"
]
},
{
Expand Down Expand Up @@ -328,11 +334,18 @@
"source": [
"!bash scripts/workflow.sh"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "bsstutorials",
"language": "python",
"name": "python3"
},
Expand All @@ -345,8 +358,7 @@
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
"pygments_lexer": "ipython3"
}
},
"nbformat": 4,
Expand Down
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