Merge pull request #106 from openforcefield/sage-2.2.0

Sage 2.2.0 full release

Author: amcisaac

.github/workflows/canary.yaml

@@ -30,7 +30,7 @@ jobs:
       - name: Find if any OFFXML files were added
         shell: bash -l {0}
         run: |
-          if [[ $(git diff origin/master HEAD --name-only | grep "\.offxml") ]]; then
+          if [[ $(git diff origin/main HEAD --name-only | grep "\.offxml") ]]; then
             echo "new_off_xml=true" >> $GITHUB_ENV
           fi
           echo $GITHUB_ENV
@@ -69,4 +69,4 @@ jobs:
         if: ${{ env.new_off_xml == 'true' }}
         shell: bash -l {0}
         run: |
-          git diff origin/master --name-only | grep "\.offxml" | python canary/scripts/test_hmr.py
+          git diff origin/main --name-only | grep "\.offxml" | python canary/scripts/test_hmr.py

.zenodo.json

@@ -3,12 +3,7 @@
       {
         "orcid": "0000-0002-7210-1164",
         "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
-        "name": "McIsaac, Alexandra"
-      },
-      {
-        "orcid": "0000-0002-6878-0192",
-        "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
-        "name": "Westbrook, Brent"
+        "name": "McIsaac, Alexandra R."
       },
       {
         "orcid": "0000-0001-6583-2148",
@@ -35,6 +30,26 @@
         "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
         "name": "Wang, Lily"
       },
+      {
+        "orcid": "0000-0002-6878-0192",
+        "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
+        "name": "Westbrook, Brent R."
+      },
+      {
+        "orcid": "0000-0002-1460-3983",
+        "affiliation": "Open Force Field Consortium, Open Molecular Software Foundation, Davis,  CA, USA",
+        "name": "Thompson, Matthew W."
+      },
+      {
+        "orcid": "0000-0002-2732-457X",
+        "affiliation": "Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA",
+        "name": "Osato, Meghan"
+      },
+      {
+        "orcid": "0000-0002-1736-7744",
+        "affiliation": "Open Free Energy, Open Molecular Software Foundation, Davis, CA, USA",
+        "name": "Baumann, Hannah M."
+      },
       {
         "orcid": "0000-0002-1697-2918",
         "affiliation": "Department of Chemistry, University of California Davis, Davis, CA, USA",

README.md

@@ -28,6 +28,10 @@ Details for each force field in this repository can be found in the following ta
 
 | Filename                                    | DOI                                                                                                       | FF line | Release Date  | Major format changes? |
 |---------------------------------------------|-----------------------------------------------------------------------------------------------------------|---------|---------------|-----------------------|
+| `openff-2.2.0.offxml`                       |                                                                                                           | Sage    | April 18, 2024 | No                    |
+| `openff_unconstrained-2.2.0.offxml`         |                                                                                                           | Sage    | April 18, 2024 | No                    |
+| `openff-2.2.0-rc1.offxml`                   |                                                                                                           | Sage    | March 6, 2024 | No                    |
+| `openff_unconstrained-2.2.0-rc1.offxml`     |                                                                                                           | Sage    | March 6, 2024 | No                    |
 | `openff-2.1.1.offxml`                       | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10553473.svg)](https://doi.org/10.5281/zenodo.10553473) | Sage    | Jan 22, 2024  | No                    |
 | `openff_unconstrained-2.1.1.offxml`         | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10553473.svg)](https://doi.org/10.5281/zenodo.10553473) | Sage    | Jan 22, 2024  | No                    |
 | `tip5p-1.0.0.offxml`                        | see `docs/water-models.md`                                                                                | Ports   | Nov 6, 2023   | No                    |
@@ -167,6 +171,8 @@ Force fields moving forward will be called `name-X.Y.Z`
 
 - `2024.03.0`: This release adds `openff-2.2.0-rc1.offxml` and `openff_unconstrained-2.2.0-rc1.offxml`, Sage 2.2.0 Release Candidate 1, which modifies some small ring internal angles and remedies issues with sulfamide geometries.
 
+- `2024.04.0`: This release adds `openff-2.2.0.offxml` and `openff_unconstrained-2.2.0.offxml`, Sage 2.2.0, with identical parameters to `openff-2.2.0-rc1.offxml`.
+
 #### Acknowledgements
 
 Project based on the

canary/scripts/test_hmr.py

@@ -7,7 +7,7 @@
 from simtk import openmm, unit
 from simtk.openmm import app
 
-DATA_PATH = importlib.resources.files("openforcefields") / "canary" / "data"
+DATA_PATH = importlib.resources.files("canary") / "data"
 coverage_mols = DATA_PATH / "coverage.smi"
 propyne_mols = DATA_PATH / "propynes.smi"
 
@@ -58,10 +58,10 @@ def hmr_driver(mol, ff_name):
     collision_rate = 1.0 / unit.picoseconds
     timestep = 4.0 * unit.femtoseconds
 
-    integrator = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
+    integrator = openmm.LangevinMiddleIntegrator(temperature, collision_rate, timestep)
     context = openmm.Context(system, integrator)
     mol.generate_conformers(n_conformers=1)
-    context.setPositions(mol.conformers[0])
+    context.setPositions(mol.conformers[0].to_openmm())
 
     # Run for 10 ps
     integrator.step(2500)
@@ -99,6 +99,7 @@ def hmr_driver(mol, ff_name):
                 hmr_driver(mol, ff_name)
             except NANEnergyError:
                 failed_runs.append([mol.to_smiles(), ff_name, "NaN energy"])
+
             except Exception:
                 # OpenMM's OpenMMException cannot be caught as it does not
                 # inherit from BaseException; therefore this clause may