diff --git a/ties/__init__.py b/ties/__init__.py
index 2bd6a8b..bff8871 100644
--- a/ties/__init__.py
+++ b/ties/__init__.py
@@ -1,4 +1,6 @@
 import logging
+logging.basicConfig(encoding='utf-8', level=logging.INFO)
+
 from pathlib import Path
 
 from . import cli
@@ -12,5 +14,3 @@
 from ._version import __version__
 
 __all__ = [Ligand, Protein, Pair, Config, LigandMap, Protein, __version__]
-
-logging.basicConfig(encoding='utf-8', level=logging.INFO)
\ No newline at end of file
diff --git a/ties/cli.py b/ties/cli.py
index ec093bd..02c0baa 100755
--- a/ties/cli.py
+++ b/ties/cli.py
@@ -62,7 +62,7 @@ def command_line_script():
                         help='Align the coordinates in the "END" ligand to the "INITIAL" ligand using '
                              'the generated maximum common substructure (MCS).')
     parser.add_argument("-v", "--logging-level", metavar="str or bool", dest="logging_level",
-                        type=ArgparseChecker.logging_lvl, required=False, default="WARNING",
+                        type=ArgparseChecker.logging_lvl, required=False, default="INFO",
                         help="Logging level. Can be a boolean value "
                              "(False disables logging by setting it to ERROR). "
                              "A string should specify a logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL). ")
@@ -152,6 +152,8 @@ def command_line_script():
     # initialise the config class
     args = parser.parse_args()
 
+    # set the root logger
+    logging.getLogger().setLevel(args.logging_level)
     logger.setLevel(args.logging_level)
     for handler in logger.handlers:
         handler.setLevel(args.logging_level)
diff --git a/ties/config.py b/ties/config.py
index e86757b..e66b3a0 100644
--- a/ties/config.py
+++ b/ties/config.py
@@ -92,6 +92,11 @@ def __init__(self, **kwargs):
         # assign all the initial configuration values
         self.set_configs(**kwargs)
 
+        # logging
+        self.logging_breakdown = True
+        self.logging_formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+        self.logging_level = logging.INFO
+
     @property
     def workdir(self):
         """
@@ -900,6 +905,9 @@ def get_serializable(self):
             if k in host_specific:
                 continue
 
+            if type(v) is logging.Formatter:
+                continue
+
             if type(v) is pathlib.PosixPath:
                 v = str(v)
 
diff --git a/ties/pair.py b/ties/pair.py
index 61078b6..eda022b 100644
--- a/ties/pair.py
+++ b/ties/pair.py
@@ -158,6 +158,8 @@ def superimpose(self, **kwargs):
         if starting_node_pairs:
             logger.debug(f'Starting nodes will be used: {starting_node_pairs}')
 
+        logging_key = str(self)
+
         # fixme - simplify to only take the ParmEd as input
         suptop = superimpose_topologies(ligand1_nodes.values(), ligand2_nodes.values(),
                                          disjoint_components=self.config.allow_disjoint_components,
@@ -178,6 +180,7 @@ def superimpose(self, **kwargs):
                                          starting_node_pairs=starting_node_pairs,
                                          parmed_ligA=parmed_ligA, parmed_ligZ=parmed_ligZ,
                                          starting_pair_seed=self.config.superimposition_starting_pair,
+                                         logging_key=logging_key,
                                          config=self.config)
 
         self.set_suptop(suptop, parmed_ligA, parmed_ligZ)
diff --git a/ties/topology_superimposer.py b/ties/topology_superimposer.py
index 08489b8..b9b942e 100644
--- a/ties/topology_superimposer.py
+++ b/ties/topology_superimposer.py
@@ -3166,6 +3166,7 @@ def superimpose_topologies(top1_nodes,
                            check_atom_names_unique=True,
                            starting_pairs_heuristics=True,
                            starting_pair_seed=None,
+                           logging_key=None,
                            config=None):
     """
     The main function that manages the entire process.
@@ -3174,6 +3175,12 @@ def superimpose_topologies(top1_nodes,
     - check if each molecule topology is connected
     """
 
+    if config.logging_breakdown:
+        file_log_handler = logging.FileHandler(config.workdir / f'{logging_key}.log')
+        file_log_handler.setLevel(config.logging_level)
+        file_log_handler.setFormatter(config.logging_formatter)
+        logger.addHandler(file_log_handler)
+
     if not ignore_charges_completely:
         whole_charge = SuperimposedTopology.validate_charges(top1_nodes, top2_nodes)
 
@@ -3382,6 +3389,9 @@ def take_largest(x, y):
     logger.info(f'Disappearing atoms: { (len(top1_nodes) - len(suptop.matched_pairs)) / len(top1_nodes) * 100:.1f}%')
     logger.info(f'Appearing atoms: { (len(top2_nodes) - len(suptop.matched_pairs)) / len(top2_nodes) * 100:.1f}%')
 
+    if config.logging_breakdown:
+        logger.removeHandler(file_log_handler)
+
     return suptop