utils: fix units of nonbondedCutoff calc

orionarcher · Jul 19, 2022 · d906eda · d906eda
1 parent 879dc81
commit d906eda
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/pymatgen/io/openmm/generators.py b/pymatgen/io/openmm/generators.py
@@ -181,7 +181,7 @@ def get_input_set(  # type: ignore
         Args:
             smiles: keys are smiles and values are number of that molecule to pack
             density: the density of the system. density OR box must be given as an argument.
-            box: list of [xlo, ylo, zlo, xhi, yhi, zhi]. density OR box must be given as an argument.
+            box: list of [xlo, ylo, zlo, xhi, yhi, zhi] with coordinates given in Angstroms. Density OR box must be given as an argument.
 
         Returns:
             an OpenMM.InputSet

diff --git a/pymatgen/io/openmm/utils.py b/pymatgen/io/openmm/utils.py
@@ -576,7 +576,9 @@ def parameterize_system(
             forcefield_omm.registerTemplateGenerator(template.generator)
 
     box_size = min(box[3] - box[0], box[4] - box[1], box[5] - box[2])
-    nonbondedCutoff = min(10, box_size // 2)
+    # NOTE: cutoff is in nm, not Angstrom!
+    # box_size is calculated in Angstrom. Convert to nm here
+    nonbondedCutoff = min(1, box_size // 20)
     # TODO: Make insensitive to input units
     periodic_box_vectors = np.array(
         [