diff --git a/biosim_extractor/helpers/metadata_utils.py b/biosim_extractor/helpers/metadata_utils.py
index c54a188..001320f 100644
--- a/biosim_extractor/helpers/metadata_utils.py
+++ b/biosim_extractor/helpers/metadata_utils.py
@@ -31,3 +31,22 @@ def round_floats(obj, decimals=3, preserve_below=1e-3):
         return {k: round_floats(v, decimals, preserve_below) for k, v in obj.items()}
 
     return obj
+
+
+def merge_metadata(existing, incoming):
+    if not existing:
+        return incoming
+    if not incoming:
+        return existing
+
+    for key, value in incoming.items():
+        if (
+            key in existing
+            and isinstance(existing[key], dict)
+            and isinstance(value, dict)
+        ):
+            merge_metadata(existing[key], value)
+        else:
+            existing[key] = value
+
+    return existing
diff --git a/biosim_extractor/metadata/populatemetadata.py b/biosim_extractor/metadata/populatemetadata.py
index a0f64fe..bfc94fc 100644
--- a/biosim_extractor/metadata/populatemetadata.py
+++ b/biosim_extractor/metadata/populatemetadata.py
@@ -10,7 +10,7 @@
 
 from biosim_extractor.amber.amberlog import AmberLogParser
 from biosim_extractor.gromacs.gromacslog import GromacsLogParser
-from biosim_extractor.helpers.metadata_utils import round_floats
+from biosim_extractor.helpers.metadata_utils import merge_metadata, round_floats
 from biosim_extractor.mdanalysis.toptraj import TopTrajParser
 from biosim_extractor.metadata.fetchschema import get_schema, update_schema
 from biosim_extractor.metadata.filemetadata import files_metadata, group_files
@@ -257,7 +257,9 @@ def populate(self):
             self.data = self.apply_mapping()
 
         if self.top_file and self.traj_file:
-            self.data = self.populate_toptraj()
+            toptraj_data = self.populate_toptraj()
+            if toptraj_data is not None:
+                self.data = merge_metadata(self.data, toptraj_data)
 
         # self.data["SimulationMetadata"]["@type"] = "SimulationMetadata"
         result = self.data["SimulationMetadata"]
@@ -526,7 +528,6 @@ def resolve_schema_inputs(args):
     mapping_path = args.mappingschema
     biosim_path = args.biosimschema
 
-    # If either path is missing, fetch a schema bundle and fill defaults.
     if not mapping_path or not biosim_path:
         bundle = (
             update_schema(
@@ -539,6 +540,7 @@ def resolve_schema_inputs(args):
                 cache_dir=args.schema_cache_dir,
             )
         )
+
         mapping_path = mapping_path or str(bundle.mapping_json)
         biosim_path = biosim_path or str(bundle.schema_yaml)