diff --git a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py b/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
index f4473127f..f518f8a0e 100644
--- a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
+++ b/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
@@ -22,22 +22,67 @@
 
 class AtomLabel:
 
-    def __init__(self, atm_label, **kwargs):
-        self.atm_label = atm_label
+    def __init__(self, atm_label: str, **kwargs):
+        """Creates an atom label object which is used for atom mapping
+        and atom type guessing.
+
+        Parameters
+        ----------
+        atm_label : str
+            The main atom label.
+        kwargs
+            The other atom label.
+        """
+        # use translations since it's faster than the alternative
+        # methods as of writing e.g. re.sub
+        translation = str.maketrans("", "", ";=")
+        self.atm_label = atm_label.translate(translation)
         self.grp_label = f""
         if kwargs:
             for k, v in kwargs.items():
-                self.grp_label += f"{k}={v};"
+                self.grp_label += f"{k}={str(v).translate(translation)};"
             self.grp_label = self.grp_label[:-1]
         self.mass = kwargs.get("mass", None)
         if self.mass is not None:
             self.mass = float(self.mass)
 
     def __eq__(self, other: object) -> bool:
+        """Used to check if atom labels are equal.
+
+        Parameters
+        ----------
+        other : AtomLabel
+            The other atom label to compare against.
+
+        Returns
+        -------
+        bool
+            True if all attributes are equal.
+
+        Raises
+        ------
+        AssertionError
+            If the other object is not an AtomLabel.
+        """
         if not isinstance(other, AtomLabel):
             AssertionError(f"{other} should be an instance of AtomLabel.")
-        if self.grp_label == other.grp_label and self.atm_label == other.atm_label:
+        if (
+            self.grp_label == other.grp_label
+            and self.atm_label == other.atm_label
+            and self.mass == other.mass
+        ):
             return True
+        else:
+            return False
+
+    def __hash__(self) -> int:
+        """
+        Returns
+        -------
+        int
+            A hash of the object in its current state.
+        """
+        return hash((self.atm_label, self.grp_label, self.mass))
 
 
 def guess_element(atm_label: str, mass: Union[float, int, None] = None) -> str:
@@ -179,6 +224,30 @@ def fill_remaining_labels(
             mapping[grp_label][atm_label] = guess_element(atm_label, label.mass)
 
 
+def mapping_to_labels(mapping: dict[str, dict[str, str]]) -> list[AtomLabel]:
+    """Converts the mapping back into a list of labels.
+
+    Parameters
+    ----------
+    mapping : dict[str, dict[str, str]]
+        The atom mapping dictionary.
+
+    Returns
+    -------
+    list[AtomLabel]
+        List of atom labels from the mapping.
+    """
+    labels = []
+    for grp_label, atm_map in mapping.items():
+        kwargs = {}
+        if grp_label:
+            for k, v in [i.split("=") for i in grp_label.split(";")]:
+                kwargs[k] = v
+        for atm_label in atm_map.keys():
+            labels.append(AtomLabel(atm_label, **kwargs))
+    return labels
+
+
 def check_mapping_valid(mapping: dict[str, dict[str, str]], labels: list[AtomLabel]):
     """Given a list of labels check that the mapping is valid.
 
@@ -194,11 +263,17 @@ def check_mapping_valid(mapping: dict[str, dict[str, str]], labels: list[AtomLab
     bool
         True if the mapping is valid.
     """
+    pattern = re.compile("^([A-Za-z]\w*=[^=;]+(;[A-Za-z]\w*=[^=;]+)*)*$")
+    if not all([pattern.match(grp_label) for grp_label in mapping.keys()]):
+        return False
+
+    if set(mapping_to_labels(mapping)) != set(labels):
+        return False
+
     for label in labels:
         grp_label = label.grp_label
         atm_label = label.atm_label
-        if grp_label not in mapping or atm_label not in mapping[grp_label]:
-            return False
         if mapping[grp_label][atm_label] not in ATOMS_DATABASE:
             return False
+
     return True
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py
index 3f34a2050..3323569b5 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py
@@ -13,6 +13,8 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
+
 from ase.io import iread, read
 from ase.io.trajectory import Trajectory as ASETrajectory
 
@@ -37,16 +39,12 @@ def parse(self):
 
         self["element_list"] = first_frame.get_chemical_symbols()
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
         for atm_label in self["element_list"]:
-            label = AtomLabel(atm_label)
-            if label not in labels:
-                labels.append(label)
-        return labels
+            yield AtomLabel(atm_label)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AtomMappingConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AtomMappingConfigurator.py
index 9ca6e5cda..c82ea71ab 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/AtomMappingConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/AtomMappingConfigurator.py
@@ -53,10 +53,10 @@ def configure(self, value) -> None:
 
         file_configurator = self._configurable[self._dependencies["input_file"]]
         if not file_configurator._valid:
-            self.error_status = "Input file not selected."
+            self.error_status = "Input file not selected or valid."
             return
 
-        labels = file_configurator.get_atom_labels()
+        labels = file_configurator.labels
         try:
             fill_remaining_labels(value, labels)
         except AttributeError:
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py
index 9c507f019..33bd20fe5 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py
@@ -13,12 +13,13 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
 import re
+
 import numpy as np
 
 from MDANSE.Core.Error import Error
 from MDANSE.Framework.AtomMapping import AtomLabel
-
 from .FileWithAtomDataConfigurator import FileWithAtomDataConfigurator
 from MDANSE.MLogging import LOG
 
@@ -186,16 +187,12 @@ def parse(self):
             except:
                 LOG.error(f"LAMMPS ConfigFileConfigurator failed to find a unit cell")
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
         for idx, mass in self["elements"]:
-            label = AtomLabel(str(idx), mass=mass)
-            if label not in labels:
-                labels.append(label)
-        return labels
+            yield AtomLabel(str(idx), mass=mass)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/FieldFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/FieldFileConfigurator.py
index 9c44341b7..de7308373 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/FieldFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/FieldFileConfigurator.py
@@ -13,6 +13,7 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
 import re
 
 import numpy as np
@@ -23,7 +24,6 @@
 )
 from MDANSE.Core.Error import Error
 from MDANSE.Framework.AtomMapping import get_element_from_mapping, AtomLabel
-
 from .FileWithAtomDataConfigurator import FileWithAtomDataConfigurator
 
 
@@ -114,20 +114,16 @@ def parse(self):
 
             first = last + 1
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
         for mol_name, _, atomic_contents, masses, _ in self["molecules"]:
             for atm_label, mass in zip(atomic_contents, masses):
-                label = AtomLabel(atm_label, molecule=mol_name, mass=mass)
-                if label not in labels:
-                    labels.append(label)
-        return labels
+                yield AtomLabel(atm_label, molecule=mol_name, mass=mass)
 
     def get_atom_charges(self) -> np.ndarray:
         """Returns an array of partial electric charges
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py
index 5e29ab12c..ba5228358 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py
@@ -13,6 +13,7 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
 from abc import abstractmethod
 import traceback
 
@@ -37,6 +38,12 @@ def configure(self, filepath: str) -> None:
             self.parse()
         except Exception as e:
             self.error_status = f"File parsing error {e}: {traceback.format_exc()}"
+            return
+
+        self.labels = self.unique_labels()
+        if len(self.labels) == 0:
+            self.error_status = f"Unable to generate atom labels"
+            return
 
     @abstractmethod
     def parse(self) -> None:
@@ -44,6 +51,14 @@ def parse(self) -> None:
         pass
 
     @abstractmethod
-    def get_atom_labels(self) -> list[AtomLabel]:
-        """Return the atoms labels in the file."""
-        pass
+    def atom_labels(self) -> Iterable[AtomLabel]:
+        """Yields atom labels"""
+
+    def unique_labels(self) -> list[AtomLabel]:
+        """
+        Returns
+        -------
+        list[AtomLabel]
+            An ordered list of atom labels.
+        """
+        return list(set(self.atom_labels()))
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/CoordinateFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py
similarity index 66%
rename from MDANSE/Src/MDANSE/Framework/Configurators/CoordinateFileConfigurator.py
rename to MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py
index da654cc2f..51c8da812 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/CoordinateFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py
@@ -13,17 +13,15 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-import ast
-import os
 from typing import Union
 
 import MDAnalysis as mda
 
-from MDANSE import PLATFORM
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
+from .MultiInputFileConfigurator import MultiInputFileConfigurator
 
 
-class CoordinateFileConfigurator(IConfigurator):
+class MDAnalysisCoordinateFileConfigurator(MultiInputFileConfigurator):
 
     _default = ("", "AUTO")
 
@@ -41,46 +39,7 @@ def configure(self, setting: tuple[Union[str, list], str]):
             string of the coordinate file format.
         """
         values, format = setting
-
-        self["values"] = self._default
-        self._original_input = values
-
-        if type(values) is str:
-            if values:
-                try:
-                    values = ast.literal_eval(values)
-                except (SyntaxError, ValueError) as e:
-                    self.error_status = f"Unable to evaluate string: {e}"
-                    return
-                if type(values) is not list:
-                    self.error_status = (
-                        f"Input values should be able to be evaluated as a list"
-                    )
-                    return
-            else:
-                values = []
-
-        if type(values) is list:
-            if not all([type(value) is str for value in values]):
-                self.error_status = f"Input values should be a list of str"
-                return
-        else:
-            self.error_status = f"Input values should be able to be evaluated as a list"
-            return
-
-        values = [PLATFORM.get_path(value) for value in values]
-
-        none_exist = []
-        for value in values:
-            if not os.path.isfile(value):
-                none_exist.append(value)
-
-        if none_exist:
-            self.error_status = f"The files {', '.join(none_exist)} do not exist."
-            return
-
-        self["values"] = values
-        self["filenames"] = values
+        super().configure(values)
 
         if format == "AUTO" or not self["filenames"]:
             self["format"] = None
@@ -95,7 +54,7 @@ def configure(self, setting: tuple[Union[str, list], str]):
         if topology_configurator._valid:
             try:
                 if len(self["filenames"]) <= 1 or self["format"] is None:
-                    traj = mda.Universe(
+                    _ = mda.Universe(
                         topology_configurator["filename"],
                         *self["filenames"],
                         format=self["format"],
@@ -103,7 +62,7 @@ def configure(self, setting: tuple[Union[str, list], str]):
                     ).trajectory
                 else:
                     coord_files = [(i, self["format"]) for i in self["filenames"]]
-                    traj = mda.Universe(
+                    _ = mda.Universe(
                         topology_configurator["filename"],
                         coord_files,
                         topology_format=topology_configurator["format"],
@@ -116,8 +75,6 @@ def configure(self, setting: tuple[Union[str, list], str]):
                 self.error_status = "Requires valid topology file."
                 return
 
-        self.error_status = "OK"
-
     @property
     def wildcard(self):
         return self._wildcard
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/TopologyFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py
similarity index 78%
rename from MDANSE/Src/MDANSE/Framework/Configurators/TopologyFileConfigurator.py
rename to MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py
index 64c820e47..c454dc99c 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/TopologyFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py
@@ -13,13 +13,15 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
+
 import MDAnalysis as mda
 
 from MDANSE.Framework.AtomMapping import AtomLabel
 from .FileWithAtomDataConfigurator import FileWithAtomDataConfigurator
 
 
-class TopologyFileConfigurator(FileWithAtomDataConfigurator):
+class MDAnalysisTopologyFileConfigurator(FileWithAtomDataConfigurator):
 
     _default = ("", "AUTO")
 
@@ -51,23 +53,26 @@ def parse(self) -> None:
             self["filename"], topology_format=self["format"]
         ).atoms
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
+        args = []
+        for arg in ["element", "name", "type", "resname", "mass"]:
+            if hasattr(self.atoms[0], arg):
+                args.append(arg)
+        if len(args) == 0:
+            yield from []
+            return
+
         for at in self.atoms:
             kwargs = {}
-            for arg in ["element", "name", "type", "resname", "mass"]:
-                if hasattr(at, arg):
-                    kwargs[arg] = getattr(at, arg)
+            for arg in args:
+                kwargs[arg] = getattr(at, arg)
             # the first out of the list above will be the main label
             (k, main_label) = next(iter(kwargs.items()))
             kwargs.pop(k)
-            label = AtomLabel(main_label, **kwargs)
-            if label not in labels:
-                labels.append(label)
-        return labels
+            yield AtomLabel(main_label, **kwargs)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDFileConfigurator.py
index d81174c23..8e29acb50 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MDFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDFileConfigurator.py
@@ -13,6 +13,8 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
+
 import itertools
 import re
 import numpy as np
@@ -191,16 +193,12 @@ def close(self):
         """Closes the file."""
         self["instance"].close()
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
         for atm_label, _ in self["atoms"]:
-            label = AtomLabel(atm_label)
-            if label not in labels:
-                labels.append(label)
-        return labels
+            yield AtomLabel(atm_label)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py
new file mode 100644
index 000000000..e3bb891d5
--- /dev/null
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py
@@ -0,0 +1,58 @@
+#    This file is part of MDANSE.
+#
+#    MDANSE is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+import mdtraj as md
+
+from MDANSE.Framework.Configurators.FloatConfigurator import FloatConfigurator
+
+
+class MDTrajTimeStepConfigurator(FloatConfigurator):
+
+    _default = 0.0
+
+    def configure(self, value):
+        # if the value is not valid then we use the MDTraj
+        # default values which maybe the time step in the inputted
+        # files or 1 ps
+        try:
+            value = float(value)
+        except (TypeError, ValueError):
+            pass
+
+        if value is None or value == "" or value == 0.0:
+            coord_conf = self._configurable[self._dependencies["coordinate_files"]]
+            top_conf = self._configurable[self._dependencies["topology_file"]]
+            if coord_conf._valid and top_conf._valid:
+                traj_files = coord_conf["filenames"]
+                top_file = top_conf["filename"]
+                try:
+                    if top_file:
+                        traj = md.load(traj_files, top=top_file)
+                    else:
+                        traj = md.load(traj_files)
+                    if traj.n_frames == 1:
+                        value = self._default
+                    else:
+                        value = float(traj.timestep)
+                except Exception as e:
+                    self.error_status = (
+                        f"Unable to determine a time step from MDTraj: {e}"
+                    )
+                    return
+            else:
+                self.error_status = f"Unable to determine a time step from MDTraj"
+                return
+
+        super().configure(value)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py
new file mode 100644
index 000000000..af4f3ce03
--- /dev/null
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py
@@ -0,0 +1,101 @@
+#    This file is part of MDANSE.
+#
+#    MDANSE is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+from typing import Optional, Iterable
+import traceback
+from pathlib import Path
+
+import mdtraj as md
+from mdtraj.core.trajectory import _TOPOLOGY_EXTS
+
+from MDANSE.Framework.AtomMapping import AtomLabel
+from .FileWithAtomDataConfigurator import FileWithAtomDataConfigurator
+
+
+class MDTrajTopologyFileConfigurator(FileWithAtomDataConfigurator):
+
+    def configure(self, value: Optional[str]):
+        """
+        Parameters
+        ----------
+        value : str or None
+            The path of the MDTraj topology file can be None if
+            topology information is contained in the trajectory files.
+        """
+        if not self._configurable[self._dependencies["coordinate_files"]].valid:
+            self.error_status = "Trajectory file not valid"
+            return
+
+        if not value:
+            self.error_status = "OK"
+            self["filename"] = value
+
+            extension = self._configurable[
+                self._dependencies["coordinate_files"]
+            ].extension
+
+            supported = list(i[1:] for i in _TOPOLOGY_EXTS)
+            if extension not in supported:
+                self.error_status = (
+                    f"Trajectory file does not contain topology information. "
+                    f"File '{extension}' not support should be one of the following: {supported}"
+                )
+                return
+
+            try:
+                self.parse()
+            except Exception as e:
+                self.error_status = f"File parsing error {e}: {traceback.format_exc()}"
+                return
+
+            self.labels = self.unique_labels()
+            if len(self.labels) == 0:
+                self.error_status = f"Unable to generate atom labels"
+
+        else:
+            extension = "".join(Path(value).suffixes)[1:]
+            supported = list(i[1:] for i in _TOPOLOGY_EXTS)
+            if extension not in supported:
+                self.error_status = f"File '{extension}' not support should be one of the following: {supported}"
+                return
+            super().configure(value)
+
+    def parse(self) -> None:
+        coord_files = self._configurable[self._dependencies["coordinate_files"]][
+            "filenames"
+        ]
+        if self["filename"]:
+            self.atoms = [
+                at for at in md.load(coord_files, top=self["filename"]).topology.atoms
+            ]
+
+        else:
+            self.atoms = [at for at in md.load(coord_files).topology.atoms]
+
+    def atom_labels(self) -> Iterable[AtomLabel]:
+        """
+        Yields
+        ------
+        AtomLabel
+            An atom label.
+        """
+        for at in self.atoms:
+            yield AtomLabel(
+                at.name,
+                symbol=at.element.symbol,
+                residue=at.residue.name,
+                number=at.element.number,
+                mass=at.element.mass,
+            )
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py
new file mode 100644
index 000000000..06632d17f
--- /dev/null
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py
@@ -0,0 +1,37 @@
+#    This file is part of MDANSE.
+#
+#    MDANSE is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+from pathlib import Path
+
+from mdtraj.formats.registry import FormatRegistry
+
+from .MultiInputFileConfigurator import MultiInputFileConfigurator
+
+
+class MDTrajTrajectoryFileConfigurator(MultiInputFileConfigurator):
+
+    def configure(self, value):
+        super().configure(value)
+
+        extensions = {"".join(Path(value).suffixes)[1:] for value in self["values"]}
+        if len(extensions) != 1:
+            self.error_status = f"Files should be of a single format."
+            return
+        self.extension = next(iter(extensions))
+
+        supported = list(i[1:] for i in FormatRegistry.loaders.keys())
+        if self.extension not in supported:
+            self.error_status = f"File '{self.extension}' not support should be one of the following: {supported}"
+            return
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py
new file mode 100644
index 000000000..59497623f
--- /dev/null
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py
@@ -0,0 +1,102 @@
+#    This file is part of MDANSE.
+#
+#    MDANSE is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+import ast
+import os
+from typing import Union
+
+from MDANSE import PLATFORM
+from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
+
+
+class MultiInputFileConfigurator(IConfigurator):
+
+    _default = ""
+
+    def __init__(self, name, wildcard="All files (*)", **kwargs):
+        IConfigurator.__init__(self, name, **kwargs)
+        self._wildcard = wildcard
+
+    def configure(self, setting: Union[str, list]):
+        """
+        Parameters
+        ----------
+        setting : Union[str, list]
+            A list of file names or a string of the list which can be
+            converted to a list using literal_eval and a string of the
+            coordinate file format.
+        """
+        values = setting
+        self["values"] = self._default
+        self._original_input = values
+
+        if type(values) is str:
+            if values:
+                try:
+                    # some issues when \ is used in the path as this
+                    # can be interpreted as an escape character by
+                    # literal_eval, on windows we can use \ or / so lets
+                    # just swap them here
+                    values = ast.literal_eval(values.replace("\\", "/"))
+                except (SyntaxError, ValueError) as e:
+                    self.error_status = f"Unable to evaluate string: {e}"
+                    return
+                if type(values) is not list:
+                    self.error_status = (
+                        f"Input values should be able to be evaluated as a list"
+                    )
+                    return
+            else:
+                values = []
+
+        if type(values) is list:
+            if not all([type(value) is str for value in values]):
+                self.error_status = f"Input values should be a list of str"
+                return
+        else:
+            self.error_status = f"Input values should be able to be evaluated as a list"
+            return
+
+        values = [PLATFORM.get_path(value) for value in values]
+
+        none_exist = []
+        for value in values:
+            if not os.path.isfile(value):
+                none_exist.append(value)
+
+        if none_exist:
+            self.error_status = f"The files {', '.join(none_exist)} do not exist."
+            return
+
+        self["values"] = values
+        self["filenames"] = values
+        self.error_status = "OK"
+
+    @property
+    def wildcard(self):
+        return self._wildcard
+
+    def get_information(self) -> str:
+        """
+        Returns
+        -------
+        str
+           Input file names.
+        """
+        try:
+            filenames = self["value"]
+        except KeyError:
+            filenames = ["None"]
+        return f"Input files: {', '.join(filenames)}.\n"
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py
index 0d857d11c..85d889e3e 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/XDATCARFileConfigurator.py
@@ -13,6 +13,8 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
+
 import numpy as np
 
 from MDANSE.Core.Error import Error
@@ -133,16 +135,12 @@ def read_step(self, step):
     def close(self):
         self["instance"].close()
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
         for symbol in self["atoms"]:
-            label = AtomLabel(symbol)
-            if label not in labels:
-                labels.append(label)
-        return labels
+            yield AtomLabel(symbol)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py
index 9c714ae6b..7ddc7b18b 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/XTDFileConfigurator.py
@@ -13,6 +13,7 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
 import collections
 import xml.etree.ElementTree as ElementTree
 
@@ -186,19 +187,15 @@ def build_chemical_system(self, aliases):
         realConf.fold_coordinates()
         self._chemicalSystem.configuration = realConf
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
         for info in self._atoms.values():
-            label = AtomLabel(info["element"], type=info["atom_name"])
-            if label not in labels:
-                labels.append(label)
-        return labels
+            yield AtomLabel(info["element"], type=info["atom_name"])
 
     def get_atom_charges(self) -> np.ndarray:
         """Returns an array of partial electric charges
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/XYZFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/XYZFileConfigurator.py
index b56452f7c..ec5ff900f 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/XYZFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/XYZFileConfigurator.py
@@ -13,7 +13,9 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
+from typing import Iterable
 import re
+
 import numpy as np
 
 from MDANSE.Core.Error import Error
@@ -140,16 +142,12 @@ def close(self):
         """Closes the file that was, until now, open for reading."""
         self["instance"].close()
 
-    def get_atom_labels(self) -> list[AtomLabel]:
+    def atom_labels(self) -> Iterable[AtomLabel]:
         """
-        Returns
-        -------
-        list[AtomLabel]
-            An ordered list of atom labels.
+        Yields
+        ------
+        AtomLabel
+            An atom label.
         """
-        labels = []
         for atm_label in self["atoms"]:
-            label = AtomLabel(atm_label)
-            if label not in labels:
-                labels.append(label)
-        return labels
+            yield AtomLabel(atm_label)
diff --git a/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py b/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py
index 9efd2b9dc..c9368e624 100644
--- a/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py
+++ b/MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py
@@ -42,7 +42,7 @@ class MDAnalysis(Converter):
     label = "MDAnalysis"
     settings = collections.OrderedDict()
     settings["topology_file"] = (
-        "TopologyFileConfigurator",
+        "MDAnalysisTopologyFileConfigurator",
         {
             "wildcard": "All files (*)",
             "default": "INPUT_FILENAME",
@@ -50,7 +50,7 @@ class MDAnalysis(Converter):
         },
     )
     settings["coordinate_files"] = (
-        "CoordinateFileConfigurator",
+        "MDAnalysisCoordinateFileConfigurator",
         {
             "wildcard": "All files (*)",
             "default": "",
diff --git a/MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py b/MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py
new file mode 100644
index 000000000..cdd1b9c57
--- /dev/null
+++ b/MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py
@@ -0,0 +1,210 @@
+#    This file is part of MDANSE.
+#
+#    MDANSE is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+import collections
+
+import mdtraj as md
+
+from MDANSE.MolecularDynamics.Trajectory import TrajectoryWriter
+from MDANSE.Framework.Converters.Converter import Converter
+from MDANSE.Chemistry.ChemicalEntity import ChemicalSystem, Atom
+from MDANSE.Framework.AtomMapping import get_element_from_mapping
+from MDANSE.MolecularDynamics.Configuration import (
+    PeriodicRealConfiguration,
+    RealConfiguration,
+)
+from MDANSE.MolecularDynamics.UnitCell import UnitCell
+
+
+class MDTraj(Converter):
+    """Using MDTraj, read the MD trajectory and write the data out to
+    the MDT file. MDTraj reads MD trajectories by specifying
+    trajectory files and optionally a topology file. Multiple files can
+    be used for the trajectory files so that trajectories will be
+    stitched together.
+    """
+
+    label = "MDTraj"
+    settings = collections.OrderedDict()
+
+    settings["coordinate_files"] = (
+        "MDTrajTrajectoryFileConfigurator",
+        {
+            "wildcard": "All files (*)",
+            "default": '["INPUT_FILENAME"]',
+            "label": "Trajectory files",
+        },
+    )
+    settings["topology_file"] = (
+        "MDTrajTopologyFileConfigurator",
+        {
+            "wildcard": "All files (*)",
+            "default": "",
+            "label": "Topology file (optional)",
+            "dependencies": {"coordinate_files": "coordinate_files"},
+        },
+    )
+    settings["atom_aliases"] = (
+        "AtomMappingConfigurator",
+        {
+            "default": "{}",
+            "label": "Atom mapping",
+            "dependencies": {"input_file": "topology_file"},
+        },
+    )
+    settings["time_step"] = (
+        "MDTrajTimeStepConfigurator",
+        {
+            "label": "Time step (ps)",
+            "default": 0.0,
+            "mini": 0.0,
+            "dependencies": {
+                "coordinate_files": "coordinate_files",
+                "topology_file": "topology_file",
+            },
+        },
+    )
+    settings["fold"] = (
+        "BooleanConfigurator",
+        {"default": False, "label": "Fold coordinates into box"},
+    )
+    settings["discard_overlapping_frames"] = (
+        "BooleanConfigurator",
+        {"default": False, "label": "Discard overlapping frames"},
+    )
+    settings["output_files"] = (
+        "OutputTrajectoryConfigurator",
+        {
+            "label": "MDANSE trajectory (filename, format)",
+            "formats": ["MDTFormat"],
+            "root": "config_file",
+        },
+    )
+
+    def initialize(self):
+        """Load the trajectory using MDTraj and create the
+        trajectory writer.
+        """
+        coord_files = self.configuration["coordinate_files"]["filenames"]
+        top_file = self.configuration["topology_file"]["filename"]
+        if top_file:
+            self.traj = md.load(
+                coord_files,
+                top=top_file,
+                discard_overlapping_frames=self.configuration[
+                    "discard_overlapping_frames"
+                ]["value"],
+            )
+        else:
+            self.traj = md.load(
+                coord_files,
+                discard_overlapping_frames=self.configuration[
+                    "discard_overlapping_frames"
+                ]["value"],
+            )
+
+        self.numberOfSteps = self.traj.n_frames
+
+        self._chemical_system = ChemicalSystem()
+        for at in self.traj.topology.atoms:
+            element = get_element_from_mapping(
+                self.configuration["atom_aliases"]["value"],
+                at.name,
+                symbol=at.element.symbol,
+                residue=at.residue.name,
+                number=at.element.number,
+                mass=at.element.mass,
+            )
+            self._chemical_system.add_chemical_entity(
+                Atom(symbol=element, name=at.name)
+            )
+
+        kwargs = {
+            "positions_dtype": self.configuration["output_files"]["dtype"],
+            "chunking_limit": self.configuration["output_files"]["chunk_size"],
+            "compression": self.configuration["output_files"]["compression"],
+        }
+        self._trajectory = TrajectoryWriter(
+            self.configuration["output_files"]["file"],
+            self._chemical_system,
+            self.numberOfSteps,
+            **kwargs
+        )
+        super().initialize()
+
+    def run_step(self, index: int):
+        """For the given frame, read the MDTraj trajectory data,
+        convert and write it out to the MDT file.
+
+        Parameters
+        ----------
+        index : int
+            The frame index.
+
+        Returns
+        -------
+        tuple[int, None]
+            A tuple of the job index and None.
+        """
+        if self.traj.unitcell_vectors is None:
+            conf = RealConfiguration(
+                self._trajectory._chemical_system,
+                self.traj.xyz[index],
+            )
+        else:
+            conf = PeriodicRealConfiguration(
+                self._trajectory._chemical_system,
+                self.traj.xyz[index],
+                UnitCell(
+                    self.traj.unitcell_vectors[index],
+                ),
+            )
+            if self.configuration["fold"]["value"]:
+                conf.fold_coordinates()
+
+        self._trajectory._chemical_system.configuration = conf
+
+        # TODO as of 11/12/2024 MDTraj does not read velocity data
+        #  there is a discussion about this on GitHub
+        #  (https://github.com/mdtraj/mdtraj/issues/1824).
+        #  It doesn't look like they have any plans to add this but if
+        #  they change their minds then we should update our code to
+        #  support this.
+
+        if self.numberOfSteps == 1:
+            time = 0
+        else:
+            if float(self.configuration["time_step"]["value"]) == 0.0:
+                time = index * self.traj.timestep
+            else:
+                time = index * float(self.configuration["time_step"]["value"])
+
+        self._trajectory.dump_configuration(
+            time,
+            units={
+                "time": "ps",
+                "unit_cell": "nm",
+                "coordinates": "nm",
+            },
+        )
+
+        return index, None
+
+    def combine(self, index, x):
+        pass
+
+    def finalize(self):
+        self._trajectory.close()
+        super(MDTraj, self).finalize()
diff --git a/MDANSE/Tests/UnitTests/AtomMapping/test_atom_mapping.py b/MDANSE/Tests/UnitTests/AtomMapping/test_atom_mapping.py
index f5d2a12a5..5ab015fcd 100644
--- a/MDANSE/Tests/UnitTests/AtomMapping/test_atom_mapping.py
+++ b/MDANSE/Tests/UnitTests/AtomMapping/test_atom_mapping.py
@@ -127,12 +127,48 @@ def test_fill_remaining_labels_fill_mapping_correctly_missing_mapping():
     assert mapping == {"molecule=mol1": {"label1": "C", "C1": "C"}}
 
 
-def test_check_mapping_valid_as_elements_are_correct():
+def test_check_mapping_valid_as_elements_are_correct_1():
     labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
     mapping = {"molecule=mol1": {"label1": "C", "C1": "C"}}
     assert check_mapping_valid(mapping, labels)
 
 
+def test_check_mapping_valid_as_elements_are_correct_2():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule=mol1": {"C1": "C", "label1": "C"}}
+    assert check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_valid_as_elements_are_correct_3():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol2")]
+    mapping = {"molecule=mol1": {"label1": "C"}, "molecule=mol2": {"C1": "C"}}
+    assert check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_valid_as_elements_are_correct_4():
+    labels = [AtomLabel("label1", type="1*"), AtomLabel("C1", type="2*")]
+    mapping = {"type=1*": {"label1": "C"}, "type=2*": {"C1": "C"}}
+    assert check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_valid_as_elements_are_correct_5():
+    labels = [AtomLabel("label1", mass="12"), AtomLabel("C1", mass="13")]
+    mapping = {"mass=12": {"label1": "C"}, "mass=13": {"C1": "C"}}
+    assert check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_valid_as_elements_are_correct_6():
+    labels = [AtomLabel("label=1", molecule="mol=1"), AtomLabel("C=1", molecule="mol=2")]
+    mapping = {"molecule=mol1": {"label1": "C"}, "molecule=mol2": {"C1": "C"}}
+    assert check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_valid_as_elements_are_correct_7():
+    labels = [AtomLabel("label=1"), AtomLabel("C=1")]
+    mapping = {"": {"label1": "C", "C1": "C"}}
+    assert check_mapping_valid(mapping, labels)
+
+
 def test_check_mapping_not_valid_as_elements_not_correct():
     labels = [
         AtomLabel("label1", molecule="mol1"),
@@ -142,10 +178,76 @@ def test_check_mapping_not_valid_as_elements_not_correct():
     assert not check_mapping_valid(mapping, labels)
 
 
-def test_check_mapping_not_valid_due_to_missing_mappings():
+def test_check_mapping_not_valid_due_to_missing_mappings_1():
     labels = [
         AtomLabel("label1", molecule="mol1"),
         AtomLabel("label2", molecule="mol1"),
     ]
     mapping = {"molecule=mol1": {"label1": "C"}}
     assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_missing_mappings_2():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol2")]
+    mapping = {"molecule=mol1": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_incorrect_keys_1():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule=mol1": {"label1": "C", "label2": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_incorrect_keys_2():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule=mol1": {"label1": "C", "C1": "C", "label2": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_1():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule==mol1": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_2():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule===mol1": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_3():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule=mol1;": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_4():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {";molecule=mol1": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_5():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule;=mol1": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_6():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"mole;cule=mol1": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_7():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol1")]
+    mapping = {"molecule=mo;l1": {"label1": "C", "C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
+
+
+def test_check_mapping_not_valid_due_to_bad_keys_8():
+    labels = [AtomLabel("label1", molecule="mol1"), AtomLabel("C1", molecule="mol2")]
+    mapping = {"molecule=mol1": {"label1": "C"}, "molec;ule=mol2": {"C1": "C"}}
+    assert not check_mapping_valid(mapping, labels)
diff --git a/MDANSE/Tests/UnitTests/test_converter.py b/MDANSE/Tests/UnitTests/test_converter.py
index f494d5292..b540e3df3 100644
--- a/MDANSE/Tests/UnitTests/test_converter.py
+++ b/MDANSE/Tests/UnitTests/test_converter.py
@@ -544,3 +544,26 @@ def test_mdanalysis_conversion_file_exists_and_loads_up_successfully(compression
     assert os.path.exists(temp_name + ".log")
     assert os.path.isfile(temp_name + ".log")
     os.remove(temp_name + ".log")
+
+
+@pytest.mark.parametrize("compression", ["none", "gzip", "lzf"])
+def test_mdtraj_conversion_file_exists_and_loads_up_successfully(compression):
+    temp_name = tempfile.mktemp()
+
+    parameters = {
+        "topology_file": hem_cam_pdb,
+        "coordinate_files": [hem_cam_dcd],
+        "output_files": (temp_name, 64, 128, compression, "INFO"),
+    }
+
+    mdanalysis = Converter.create("MDTraj")
+    mdanalysis.run(parameters, status=True)
+
+    HDFTrajectoryConfigurator("trajectory").configure(temp_name + ".mdt")
+
+    assert os.path.exists(temp_name + ".mdt")
+    assert os.path.isfile(temp_name + ".mdt")
+    os.remove(temp_name + ".mdt")
+    assert os.path.exists(temp_name + ".log")
+    assert os.path.isfile(temp_name + ".log")
+    os.remove(temp_name + ".log")
diff --git a/MDANSE/Tests/UnitTests/test_ijob.py b/MDANSE/Tests/UnitTests/test_ijob.py
index 04b4c3549..598ecfaf3 100644
--- a/MDANSE/Tests/UnitTests/test_ijob.py
+++ b/MDANSE/Tests/UnitTests/test_ijob.py
@@ -60,6 +60,7 @@
     "ImprovedASE",
     "LAMMPS",
     "MDAnalysis",
+    "MDTraj",
     "VASP",
     "CHARMM",
     "NAMD",
diff --git a/MDANSE/pyproject.toml b/MDANSE/pyproject.toml
index c9899f3a3..34a2d630f 100644
--- a/MDANSE/pyproject.toml
+++ b/MDANSE/pyproject.toml
@@ -35,7 +35,8 @@ dependencies = [
     "h5py",
     "ase",
     "rdkit",
-    "MDAnalysis"
+    "MDAnalysis",
+    "mdtraj"
 ]
 
 # dynamic = ["version", "description"]
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomMappingWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomMappingWidget.py
index 912af9b1a..bc36997af 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomMappingWidget.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/AtomMappingWidget.py
@@ -64,7 +64,6 @@ def __init__(
         self._field = field
 
         self._file_widget = field_widget
-        self._file_widget.value_changed.connect(self.update_helper)
 
         self.layout = QVBoxLayout()
         buffer_0 = QWidget(self)
@@ -109,11 +108,14 @@ def update_helper(self) -> None:
         if not self._file_widget._configurator.valid:
             return
 
-        self.labels = self._file_widget._configurator.get_atom_labels()
+        self.labels = self._file_widget._configurator.labels
         for i, label in enumerate(self.labels):
             w0 = QLabel(label.grp_label.replace(";", "\n"))
             w1 = QLabel(label.atm_label)
             w2 = QComboBox()
+            # this combobox can be slow without this policy since we
+            # are adding alot of items
+            w2.setSizeAdjustPolicy(w2.AdjustToMinimumContentsLengthWithIcon)
             w2.addItems(self.all_symbols)
             self.mapping_widgets.append((w0, w1, w2))
             self.mapping_layout.addWidget(w0, i, 0)
@@ -202,9 +204,13 @@ def update_helper_button(self) -> None:
         """
         if self._file_widget._configurator.valid:
             self.helper_button.setEnabled(True)
+            self.helper.update_helper()
+            self.helper.apply()
         else:
             self.helper_button.setEnabled(False)
-        self.helper.apply()
+            self.helper.close()
+            self.helper.clear_panel()
+            self.helper.apply()
 
     @Slot()
     def helper_dialog(self) -> None:
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisCoordinateFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisCoordinateFileWidget.py
new file mode 100644
index 000000000..699ff6c46
--- /dev/null
+++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisCoordinateFileWidget.py
@@ -0,0 +1,41 @@
+#    This file is part of MDANSE_GUI.
+#
+#    MDANSE_GUI is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+import MDAnalysis as mda
+from qtpy.QtWidgets import QFileDialog
+
+from .MDAnalysisTopologyFileWidget import MDAnalysisTopologyFileWidget
+from .MultiInputFileWidget import MultiInputFileWidget
+
+
+class MDAnalysisCoordinateFileWidget(
+    MultiInputFileWidget, MDAnalysisTopologyFileWidget
+):
+
+    def __init__(self, *args, file_dialog=QFileDialog.getOpenFileNames, **kwargs):
+        super().__init__(
+            *args,
+            file_dialog=file_dialog,
+            format_options=sorted(mda._READERS.keys()),
+            **kwargs,
+        )
+        for widget in self.parent()._widgets:
+            if (
+                widget._configurator
+                is self._configurator._configurable[
+                    self._configurator._dependencies["input_file"]
+                ]
+            ):
+                widget.value_changed.connect(self.updateValue)
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTimeStepWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py
similarity index 54%
rename from MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTimeStepWidget.py
rename to MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py
index 6779c4555..0457e089c 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTimeStepWidget.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisMDTrajTimeStepWidget.py
@@ -13,13 +13,10 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-import MDAnalysis as mda
-
-from MDANSE.MLogging import LOG
 from .FloatWidget import FloatWidget
 
 
-class MDAnalysisTimeStepWidget(FloatWidget):
+class MDAnalysisMDTrajTimeStepWidget(FloatWidget):
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
@@ -50,36 +47,8 @@ def update_from_files(self) -> None:
         """Updates the time step field from the topology and coordinates
         files if possible else set it back to the default value.
         """
-        if (
-            self._topology_file_widget._configurator.valid
-            and self._coordinates_file_widget._configurator.valid
-        ):
-            try:
-                coord_format = self._coordinates_file_widget._configurator["format"]
-                coord_files = self._coordinates_file_widget._configurator["filenames"]
-
-                if len(coord_files) <= 1 or coord_format is None:
-                    value = mda.Universe(
-                        self._topology_file_widget._configurator["filename"],
-                        *coord_files,
-                        format=coord_format,
-                        topology_format=self._topology_file_widget._configurator[
-                            "format"
-                        ],
-                    ).trajectory.ts.dt
-                else:
-                    coord_files = [(i, coord_format) for i in coord_files]
-                    value = mda.Universe(
-                        self._topology_file_widget._configurator["filename"],
-                        coord_files,
-                        topology_format=self._topology_file_widget._configurator[
-                            "format"
-                        ],
-                    ).trajectory.ts.dt
-
-                self._field.setText(str(value))
-                return
-            except Exception as e:
-                LOG.warning(f"Failed to determine time step from MDAnalysis: {e}")
-
-        self._field.setText(str(self._default_value))
+        self._configurator.configure(None)
+        if self._configurator._valid:
+            self._field.setText(str(self._configurator["value"]))
+        else:
+            self._field.setText(str(self._default_value))
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/TopologyFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTopologyFileWidget.py
similarity index 97%
rename from MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/TopologyFileWidget.py
rename to MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTopologyFileWidget.py
index c2826f46b..2f3ea8880 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/TopologyFileWidget.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDAnalysisTopologyFileWidget.py
@@ -20,7 +20,7 @@
 from .InputFileWidget import InputFileWidget
 
 
-class TopologyFileWidget(InputFileWidget):
+class MDAnalysisTopologyFileWidget(InputFileWidget):
 
     def __init__(self, *args, format_options=sorted(mda._PARSERS.keys()), **kwargs):
         self.format_options = ["AUTO"] + list(format_options)
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py
new file mode 100644
index 000000000..a85634f9f
--- /dev/null
+++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MDTrajTopologyFileWidget.py
@@ -0,0 +1,33 @@
+#    This file is part of MDANSE_GUI.
+#
+#    MDANSE_GUI is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+from .InputFileWidget import InputFileWidget
+
+
+class MDTrajTopologyFileWidget(InputFileWidget):
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        # file input widgets should be loaded into the _widgets list
+        # before this one
+        for widget in self.parent()._widgets:
+            if (
+                widget._configurator
+                is self._configurator._configurable[
+                    self._configurator._dependencies["coordinate_files"]
+                ]
+            ):
+                widget.value_changed.connect(self.updateValue)
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CoordinateFileWidget.py b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py
similarity index 81%
rename from MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CoordinateFileWidget.py
rename to MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py
index 3d7b1a38e..3fb641da9 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/CoordinateFileWidget.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/InputWidgets/MultiInputFileWidget.py
@@ -16,31 +16,21 @@
 import os
 from pathlib import PurePath
 
-import MDAnalysis as mda
-from qtpy.QtWidgets import QFileDialog
 from qtpy.QtCore import Slot
+from qtpy.QtWidgets import QFileDialog
 
 from MDANSE.MLogging import LOG
-from .TopologyFileWidget import TopologyFileWidget
+from .InputFileWidget import InputFileWidget
 
 
-class CoordinateFileWidget(TopologyFileWidget):
+class MultiInputFileWidget(InputFileWidget):
 
     def __init__(self, *args, file_dialog=QFileDialog.getOpenFileNames, **kwargs):
         super().__init__(
             *args,
             file_dialog=file_dialog,
-            format_options=sorted(mda._READERS.keys()),
             **kwargs,
         )
-        for widget in self.parent()._widgets:
-            if (
-                widget._configurator
-                is self._configurator._configurable[
-                    self._configurator._dependencies["input_file"]
-                ]
-            ):
-                widget.value_changed.connect(self.updateValue)
 
     @Slot()
     def valueFromDialog(self):
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py
index 25ab46e8e..4fd9291c4 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py
@@ -56,9 +56,9 @@
     "ASEFileConfigurator": InputFileWidget,
     "AseInputFileConfigurator": AseInputFileWidget,
     "ConfigFileConfigurator": InputFileWidget,
-    "CoordinateFileConfigurator": CoordinateFileWidget,
+    "MDAnalysisCoordinateFileConfigurator": MDAnalysisCoordinateFileWidget,
     "InputFileConfigurator": InputFileWidget,
-    "TopologyFileConfigurator": TopologyFileWidget,
+    "MDAnalysisTopologyFileConfigurator": MDAnalysisTopologyFileWidget,
     "MDFileConfigurator": InputFileWidget,
     "FieldFileConfigurator": InputFileWidget,
     "XDATCARFileConfigurator": InputFileWidget,
@@ -82,7 +82,10 @@
     "InstrumentResolutionConfigurator": InstrumentResolutionWidget,
     "PartialChargeConfigurator": PartialChargeWidget,
     "UnitCellConfigurator": UnitCellWidget,
-    "MDAnalysisTimeStepConfigurator": MDAnalysisTimeStepWidget,
+    "MDAnalysisTimeStepConfigurator": MDAnalysisMDTrajTimeStepWidget,
+    "MDTrajTimeStepConfigurator": MDAnalysisMDTrajTimeStepWidget,
+    "MDTrajTrajectoryFileConfigurator": MultiInputFileWidget,
+    "MDTrajTopologyFileConfigurator": MDTrajTopologyFileWidget,
 }