diff --git a/alphafold/model/config.py b/alphafold/model/config.py
index 01d6e72..43b0aab 100644
--- a/alphafold/model/config.py
+++ b/alphafold/model/config.py
@@ -991,6 +991,15 @@ class AlphaFoldConfig(base_config.BaseConfig):
   data: Optional[Data] = None
 
 
+def _set_num_ensembles(cfg: Any, name: str):
+  """Sets the number of ensembles based on the model name."""
+  num_ensembles = 8 if name in MODEL_PRESETS['monomer_casp14'] else 1
+  if 'multimer' in name:
+    cfg.model.num_ensemble_eval = num_ensembles
+  else:
+    cfg.data.eval.num_ensemble = num_ensembles
+
+
 def model_config(name: str) -> ml_collections.ConfigDict:
   """Get the ConfigDict of a CASP14 model."""
 
@@ -1001,6 +1010,7 @@ def model_config(name: str) -> ml_collections.ConfigDict:
   else:
     cfg = copy.deepcopy(CONFIG)
   cfg.update_from_flattened_dict(CONFIG_DIFFS[name])
+  _set_num_ensembles(cfg, name)
   return cfg
 
 
@@ -1016,6 +1026,7 @@ def get_model_config(name: str, frozen: bool = True) -> AlphaFoldConfig:
   )
   apply_diff_op = CONFIG_DIFF_OPS[name]
   apply_diff_op(cfg)
+  _set_num_ensembles(cfg, name)
   if frozen:
     cfg.freeze()
   return cfg
diff --git a/run_alphafold.py b/run_alphafold.py
index 0f82d85..343883a 100644
--- a/run_alphafold.py
+++ b/run_alphafold.py
@@ -474,11 +474,6 @@ def main(argv):
   _check_flag('uniprot_database_path', 'model_preset',
               should_be_set=run_multimer_system)
 
-  if FLAGS.model_preset == 'monomer_casp14':
-    num_ensemble = 8
-  else:
-    num_ensemble = 1
-
   # Check for duplicate FASTA file names.
   fasta_names = [pathlib.Path(p).stem for p in FLAGS.fasta_paths]
   if len(fasta_names) != len(set(fasta_names)):
@@ -540,10 +535,6 @@ def main(argv):
   model_names = config.MODEL_PRESETS[FLAGS.model_preset]
   for model_name in model_names:
     model_config = config.model_config(model_name)
-    if run_multimer_system:
-      model_config.model.num_ensemble_eval = num_ensemble
-    else:
-      model_config.data.eval.num_ensemble = num_ensemble
     model_params = data.get_model_haiku_params(
         model_name=model_name, data_dir=FLAGS.data_dir)
     model_runner = model.RunModel(model_config, model_params)