diff --git a/dpgen2/exploration/task/make_task_group_from_config.py b/dpgen2/exploration/task/make_task_group_from_config.py
index 2859ac8f..b11300d7 100644
--- a/dpgen2/exploration/task/make_task_group_from_config.py
+++ b/dpgen2/exploration/task/make_task_group_from_config.py
@@ -635,7 +635,8 @@ def make_lmp_task_group_from_config(
 ):
     # Work around the required conf_idx.
     # May not be a good design!!!
-    config["conf_idx"] = [] if "conf_idx" not in config else None
+    config = config.copy()
+    config.setdefault("conf_idx", [])
     config = lmp_normalize(config)
     config = config_strip_confidx(config)
     if config["type"] == "lmp-md":
diff --git a/tests/exploration/test_make_task_group_from_config.py b/tests/exploration/test_make_task_group_from_config.py
index f9fe93be..d91a99a2 100644
--- a/tests/exploration/test_make_task_group_from_config.py
+++ b/tests/exploration/test_make_task_group_from_config.py
@@ -58,6 +58,21 @@ def test_npt(self):
         )
         self.assertTrue(isinstance(tgroup, NPTTaskGroup))
 
+    def test_npt_preserves_explicit_conf_idx(self):
+        """Keep caller configuration indices intact during normalization."""
+        config = {
+            "type": "lmp-md",
+            "Ts": [100],
+            "conf_idx": [2],
+        }
+
+        tgroup = make_lmp_task_group_from_config(
+            self.numb_models, self.mass_map, config
+        )
+
+        self.assertTrue(isinstance(tgroup, NPTTaskGroup))
+        self.assertEqual(config["conf_idx"], [2])
+
     def test_template(self):
         tgroup = make_lmp_task_group_from_config(
             self.numb_models, self.mass_map, self.config_template