diff --git a/src/schnetpack/md/utils/md_config.py b/src/schnetpack/md/utils/md_config.py
index 84213da1a..16626a2ed 100644
--- a/src/schnetpack/md/utils/md_config.py
+++ b/src/schnetpack/md/utils/md_config.py
@@ -37,9 +37,13 @@ def merge_configs(
         Returns:
             DictConfig: basic config updated with entries from the overwrite config and all overrides re-applied.
         """
-
         # merge overwrite config into basic config
-        merged_config = OmegaConf.merge(base_config, overwrite_config)
+        # basic merge is not operating properly, so the basic config needs to be updated on a field by field basis
+        merged_config = copy.deepcopy(base_config)
+
+        for k, v in overwrite_config.items():
+            # force add ensures new values (e.g. temperature in RPMD integrator are still inserted into config block)
+            OmegaConf.update(merged_config, k, v, merge=True, force_add=True)
 
         # get overrides in list of lists format
         overrides_modify, overrides_delete = self._parse_overrides(overrides)