Replace ParmEd with Interchange in Amber/GROMACS example

.github/workflows/examples.yml

@@ -27,11 +27,11 @@ jobs:
           - ubuntu-latest
           - macos-latest
         cfg:
-          - python-version: 3.7
+          - python-version: 3.9
             rdkit: "true"
             openeye: "false"
 
-          - python-version: 3.7
+          - python-version: 3.9
             rdkit: "false"
             openeye: "true"
 
@@ -61,7 +61,7 @@ jobs:
           auto-activate-base: false
           miniforge-version: latest
           miniforge-variant: Mambaforge
-          use-mamba: true
+          use-mamba: false
       - uses: conda-incubator/setup-miniconda@v2.1.1
         name: Install with OpenEye toolkits
         if: ${{ matrix.cfg.rdkit == 'FALSE' && matrix.cfg.openeye == 'TRUE' }}
@@ -101,6 +101,8 @@ jobs:
       - name: Install package
         shell: bash -l {0}
         run: |
+          pip install git+https://github.com/openforcefield/openff-interchange.git@skip-drivers
+
           # Remove the packaged openff-toolkit, installed as a dependency of openmmforcefields
           conda remove --force openff-toolkit-base
           python setup.py develop --no-deps
@@ -120,13 +122,21 @@ jobs:
           fi
           pytest $PYTEST_ARGS openff/toolkit/tests/test_examples.py
 
+      - name: Run only the Amber/GROMACS notebooks
+        shell: bash -l {0}
+        run: |
+          if [[ "$RDKIT" == true ]]; then
+            pytest $NB_ARGS examples/using_smirnoff_in_amber_or_gromacs/
+          fi
+
       - name: Run example notebooks
         shell: bash -l {0}
         run: |
           if [[ "$RDKIT" == false ]]; then
             NB_ARGS+=" --ignore=examples/QCArchive_interface"
             NB_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
             NB_ARGS+=" --ignore=examples/conformer_energies"
+            NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs"
           fi
           pytest $NB_ARGS examples
 

environment.yml

@@ -3,6 +3,7 @@ name: binder-env
 channels:
   - conda-forge
   - defaults
+  - bioconda
 dependencies:
   # Let conda pull in the toolkit and its deps
   - openff-toolkit
@@ -13,3 +14,6 @@ dependencies:
   - qcportal
   - qcengine
   - openmmforcefields
+  - openff-interchange >=0.1.2
+  - gromacs
+  - lammps

examples/environment.yaml

@@ -17,3 +17,6 @@ dependencies:
   - numpy
   - openmm
   - openff-forcefields >=2.0.0
+  - openff-interchange >=0.1.2
+  - gromacs
+  - lammps

examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb → examples/using_smirnoff_in_amber_or_gromacs/convert_with_parmed.ipynb

@@ -3,6 +3,17 @@
   {
    "cell_type": "markdown",
    "metadata": {},
+   "source": [
+    " <div class=\"alert alert-block alert-info\">\n",
+    "    <b>Note:</b> \n",
+    "    Please take a look at the other notebook in the folder (<code>export_with_interchange.ipynb</code>), showcasing how to use OpenFF Interchange. Interchange is well-validated for small molecule interoperability with several formats and is in the process of replacing ParmEd in OpenFF workflows.</div>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": []
+   },
    "source": [
     "## Convert Open Forcefield System to AMBER and GROMACS input files\n",
     "\n",
@@ -82,7 +93,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true,
+    "tags": []
+   },
    "source": [
     "### Convert OpenMM System to AMBER and GROMACS files\n",
     "\n",
@@ -263,7 +277,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -277,7 +291,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,