Exclude ions from the perturbation.

OpenBioSim · Mar 13, 2024 · ddef28f · ddef28f
1 parent 243311e
commit ddef28f
Showing 1 changed file with 8 additions and 6 deletions.
diff --git a/src/somd2/runner/_somd1.py b/src/somd2/runner/_somd1.py
@@ -648,12 +648,14 @@ def _apply_pert(system, pert_file):
     # Try to apply the perturbation to each non-water molecule.
     is_pert = False
     for mol in non_waters:
-        try:
-            pert_mol = _morph.create_from_pertfile(mol, pert_file)
-            is_pert = True
-            break
-        except:
-            pass
+        # Exclude ions.
+        if mol.num_atoms() > 1:
+            try:
+                pert_mol = _morph.create_from_pertfile(mol, pert_file)
+                is_pert = True
+                break
+            except:
+                pass
 
     if not is_pert:
         raise ValueError(f"Failed to apply the perturbation in '{pert_file}'.")