Merge pull request #292 from OpenBioSim/fix_291

Fix issue #291
OpenBioSim · May 17, 2024 · 598a674 · 598a674
2 parents 240e2f1 + 1064413
commit 598a674
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Showing 2 changed files with 19 additions and 5 deletions.
diff --git a/nodes/playground/prepareFEP.ipynb b/nodes/playground/prepareFEP.ipynb
@@ -317,7 +317,10 @@
  ")\n",
  "# Create a composite system\n",
  "system1.removeMolecules(lig1)\n",
- "system1.addMolecules(merged)"
+ "system1.addMolecules(merged)\n",
+ "# Make sure the box vectors are in reduced form.\n",
+ "system1.reduceBoxVectors()\n",
+ "system1.rotateBoxVectors()"
  ]
  },
  {
@@ -336,7 +339,11 @@
  " \"merged_at_lam0.pdb\",\n",
  " merged,\n",
  " \"PDB\",\n",
- " {\"coordinates\": \"coordinates0\", \"bond\": \"bond0\", \"element\": \"element0\"},\n",
+ " property_map={\n",
+ " \"coordinates\": \"coordinates0\",\n",
+ " \"bond\": \"bond0\",\n",
+ " \"element\": \"element0\",\n",
+ " },\n",
  ")\n",
  "if is_somd2:\n",
  " BSS.Stream.save(system1, root)\n",
@@ -426,9 +433,9 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.10.11"
+ "version": "3.12.2"
  }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/nodes/playground/prepareFEP.py b/nodes/playground/prepareFEP.py
@@ -258,6 +258,9 @@ def loadMapping(mapping_file):
 # Create a composite system
 system1.removeMolecules(lig1)
 system1.addMolecules(merged)
+# Make sure the box vectors are in reduced form.
+system1.reduceBoxVectors()
+system1.rotateBoxVectors()
 
 
 # In[ ]:
@@ -273,7 +276,11 @@ def loadMapping(mapping_file):
  "merged_at_lam0.pdb",
  merged,
  "PDB",
- {"coordinates": "coordinates0", "bond": "bond0", "element": "element0"},
+ property_map={
+ "coordinates": "coordinates0",
+ "bond": "bond0",
+ "element": "element0",
+ },
 )
 if is_somd2:
  BSS.Stream.save(system1, root)