Merge pull request #163 from talagayev/Charm2024_implementation

Charm2024 implementation

Author: talagayev

CHANGELOG.md

@@ -21,6 +21,7 @@ The rules for this file:
 talagayev
 
 ### Added
+- Addition of `CHARM2024` forcefield (2025-11-03, PR #163)
 
 ### Fixed
 - Fixes import error in `visualization.ipynb` (2025-10-14, PR #159)

environment.yml

@@ -19,7 +19,7 @@ dependencies:
   - pdbfixer
   - openff-toolkit
   - openmmforcefields
-  - openmm>=8.3.0
+  - openmm>=8.3.1
   - cuda-toolkit
   - cuda-python>=11.7.1
   - mdanalysis>=2.3.0

openmmdl/openmmdl_setup/templates/configurePdbFile.html

@@ -33,6 +33,7 @@
         <option value="AMBER03">AMBER03</option>
         <option value="AMBER10">AMBER10</option>
         <option value="CHARMM36">CHARMM36</option>
+        <option value="CHARMM2024">CHARMM36 2024</option>
     </select></div>
     </div>
     <div id="waterModelRow" class="form-group">
@@ -83,7 +84,7 @@
         ["OPC", "OPC", false],
 ]
 
-var charmm36WaterModels = [
+var charmmWaterModels = [
         ["CHARMM default", "CHARMM default", true],
         ["TIP3P-PME-B", "TIP3P-PME-B", false],
         ["TIP3P-PME-F", "TIP3P-PME-F", false],
@@ -124,7 +125,9 @@
         else if (forcefield == "AMBER19")
             models = newAmberWaterModels;
         else if (forcefield == "CHARMM36")
-            models = charmm36WaterModels;
+            models = charmmWaterModels;
+        else if (forcefield == "CHARMM2024")
+            models = charmmWaterModels;
         else if (forcefield == "AMOEBA2018")
             models = amoebaWaterModels;
         else

openmmdl/openmmdl_simulation/scripts/forcefield_water.py

@@ -21,6 +21,7 @@ def ff_selection(ff):
         "AMBER03": "amber03.xml",
         "AMBER10": "amber10.xml",
         "CHARMM36": "charmm36.xml",
+        "CHARMM2024": "charmm36_2024.xml",
     }
 
     return forcefield_dict.get(ff, None)
@@ -83,6 +84,16 @@ def water_forcefield_selection(water, forcefield_selection):
                 "TIP5P": "charmm36/tip5p.xml",
                 "TIP5P-Ew": "charmm36/tip5pew.xml",
             },
+            "charmm36_2024.xml": {
+                "CHARMM default": "charmm36_2024/water.xml",
+                "TIP3P-PME-B": "charmm36_2024/tip3p-pme-b.xml",
+                "TIP3P-PME-F": "charmm36_2024/tip3p-pme-f.xml",
+                "SPC/E": "charmm36_2024/spce.xml",
+                "TIP4P-Ew": "charmm36_2024/tip4pew.xml",
+                "TIP4P-2005": "charmm36_2024/tip4p2005.xml",
+                "TIP5P": "charmm36_2024/tip5p.xml",
+                "TIP5P-Ew": "charmm36_2024/tip5pew.xml",
+            },
         }
         water_model = water_forcefields.get(forcefield_selection, {}).get(water, None)
 
@@ -122,14 +133,14 @@ def water_model_selection(water, forcefield_selection):
         if water == "TIP5P":
             return None  # 'TIP5P' is not available in 'amber19-all.xml'
         water_model = water_model_mapping.get(water)
-    elif forcefield_selection == "charmm36.xml":
+    elif forcefield_selection == "charmm36.xml" or forcefield_selection == "charmm36_2024.xml":
         charmm_water_mapping = {
             "CHARMM default": "charmm",
             "TIP3P-PME-B": "charmm",
             "TIP3P-PME-F": "charmm",
             "SPC/E": "charmm",
-            "TIP4P-Ew": "tip4pew",
-            "TIP4P-2005": "tip4pew",
+            "TIP4P-Ew": "charmm_tip4pew",
+            "TIP4P-2005": "charmm_tip4pew",
             "TIP5P": "tip5p",
             "TIP5P-Ew": "tip5p",
         }

openmmdl/tests/openmmdl_simulation/forcefield_water_test.py

@@ -117,6 +117,34 @@ def test_water_forcefield_selection():
     assert water_forcefield_selection("NonexistentFF", "charmm36.xml") is None
 
 
+    # Test cases for 'charmm36_2024.xml' force field
+    assert (
+        water_forcefield_selection("CHARMM default", "charmm36_2024.xml")
+        == "charmm36_2024/water.xml"
+    )
+    assert (
+        water_forcefield_selection("TIP3P-PME-B", "charmm36_2024.xml")
+        == "charmm36_2024/tip3p-pme-b.xml"
+    )
+    assert (
+        water_forcefield_selection("TIP3P-PME-F", "charmm36_2024.xml")
+        == "charmm36_2024/tip3p-pme-f.xml"
+    )
+    assert water_forcefield_selection("SPC/E", "charmm36_2024.xml") == "charmm36_2024/spce.xml"
+    assert (
+        water_forcefield_selection("TIP4P-Ew", "charmm36_2024.xml") == "charmm36_2024/tip4pew.xml"
+    )
+    assert (
+        water_forcefield_selection("TIP4P-2005", "charmm36_2024.xml")
+        == "charmm36_2024/tip4p2005.xml"
+    )
+    assert water_forcefield_selection("TIP5P", "charmm36_2024.xml") == "charmm36_2024/tip5p.xml"
+    assert (
+        water_forcefield_selection("TIP5P-Ew", "charmm36_2024.xml") == "charmm36_2024/tip5pew.xml"
+    )
+    assert water_forcefield_selection("NonexistentWater", "charmm36_2024.xml") is None
+    assert water_forcefield_selection("NonexistentFF", "charmm36_2024.xml") is None
+
 def test_water_model_selection():
     assert water_model_selection("TIP3P", "amber99sb.xml") == "tip3p"
     assert water_model_selection("TIP3P", "amber99sbildn.xml") == "tip3p"
@@ -162,11 +190,22 @@ def test_water_model_selection():
     assert water_model_selection("TIP3P-PME-B", "charmm36.xml") == "charmm"
     assert water_model_selection("TIP3P-PME-F", "charmm36.xml") == "charmm"
     assert water_model_selection("SPC/E", "charmm36.xml") == "charmm"
-    assert water_model_selection("TIP4P-Ew", "charmm36.xml") == "tip4pew"
-    assert water_model_selection("TIP4P-2005", "charmm36.xml") == "tip4pew"
+    assert water_model_selection("TIP4P-Ew", "charmm36.xml") == "charmm_tip4pew"
+    assert water_model_selection("TIP4P-2005", "charmm36.xml") == "charmm_tip4pew"
     assert water_model_selection("TIP5P", "charmm36.xml") == "tip5p"
     assert water_model_selection("TIP5P-Ew", "charmm36.xml") == "tip5p"
 
+    #Test new CHARMM36 2024 models
+    assert water_model_selection("CHARMM default", "charmm36_2024.xml") == "charmm"
+    assert water_model_selection("TIP3P-PME-B", "charmm36_2024.xml") == "charmm"
+    assert water_model_selection("TIP3P-PME-F", "charmm36_2024.xml") == "charmm"
+    assert water_model_selection("SPC/E", "charmm36_2024.xml") == "charmm"
+    assert water_model_selection("TIP4P-Ew", "charmm36_2024.xml") == "charmm_tip4pew"
+    assert water_model_selection("TIP4P-2005", "charmm36_2024.xml") == "charmm_tip4pew"
+    assert water_model_selection("TIP5P", "charmm36_2024.xml") == "tip5p"
+    assert water_model_selection("TIP5P-Ew", "charmm36_2024.xml") == "tip5p"
+
+    
     assert water_model_selection("TIP3P", "NonexistentFF") is None