diff --git a/ensemble_md/analysis/clustering.py b/ensemble_md/analysis/clustering.py
index bd7985eb..01621780 100644
--- a/ensemble_md/analysis/clustering.py
+++ b/ensemble_md/analysis/clustering.py
@@ -11,7 +11,7 @@
 from ensemble_md.utils.utils import run_gmx_cmd
 
 
-def cluster_traj(gmx_executable, inputs, grps, method='linkage', cutoff=0.1, suffix=None):
+def cluster_traj(gmx_executable, inputs, grps, coupled_only=True, method='linkage', cutoff=0.1, suffix=None):
     """
     Performs clustering analysis on a trajectory using the GROMACS command :code:`gmx cluster`.
     Note that only fully coupled configurations are considered.
@@ -21,27 +21,46 @@ def cluster_traj(gmx_executable, inputs, grps, method='linkage', cutoff=0.1, suf
     gmx_executable : str
         The path to the GROMACS executable.
     inputs : dict
-        A dictionary that contains the file names of the input trajectory file (XTC or TRR),
-        the configuration file (TPR or GRO), the file that contains the time series of the
-        state index, and the index file (NDX). The must include the keys :code:`traj`, :code:`config`,
-        :code:`xvg`, and :code:`index`. Note that the value for the key :code:`index` can be :code:`None`.
+        A dictionary that contains the different input files required for the clustering analysis.
+        The dictionary must have the following four keys: :code:`traj` (input trajectory file in 
+        XTC or TRR format), :code:`config` (the configuration file in TPR or GRO format),
+        :code:`xvg` (a GROMACS XVG file), and :code:`index` (an index/NDX file), with the values
+        being the paths. Note that the value of the key :code:`index` can be :code:`None`, in which
+        case the function will use a default index file generated by :code:`gmx make_ndx`. If the
+        parameter :code:`coupled_only` is set to :code:`True`, an XVG file that contains the time
+        series of the state index (e.g., :code:`dhdl.xvg`) must be provided with the key :code:`xvg`.
+        Otherwise, the key :code:`xvg` can be set to :code:`None`.
     grps : dict
         A dictionary that contains the names of the groups in the index file (NDX) for
         centering the system, calculating the RMSD, and outputting. The keys are
         :code:`center`, :code:`rmsd`, and :code:`output`.
+    coupled_only : bool
+        Whether to consider only the fully coupled configurations. The default is :code:`True`.
     method : str
         The method for clustering available for the GROMACS command :code:`gmx cluster`. The default is 'linkage'.
+        Check the GROMACS documentation for other available options.
     cutoff : float
-        The cutoff in RMSD for clustering. The default is 0.1.
+        The RMSD cutoff for clustering in nm. The default is 0.1.
     suffix : str
         The suffix for the output files. The default is :code:`None`, which means no suffix will be added.
     """
-    # First check if all specified groups are present in the index file
+    # Check if the index file is provided
+    if inputs['index'] is None:
+        print('Running gmx make_ndx to generate an index file ...')
+        args = [
+            gmx_executable, 'make_ndx',
+            '-f', inputs['config'],
+            '-o', 'index.ndx',
+        ]
+        returncode, stdout, stderr = run_gmx_cmd(args, prompt_input='q\n')
+        inputs['index'] = 'index.ndx'
+
+    # Check if the groups are present in the index file
     with open(inputs['index'], 'r') as f:
         content = f.read()
     for key in grps:
         if grps[key] not in content:
-            raise ValueError(f'The group {grps[key]} is not present in the index file.')
+            raise ValueError(f'The group {grps[key]} is not present in the provided/generated index file.')
 
     outputs = {
         'nojump': 'nojump.xtc',
@@ -61,14 +80,20 @@ def cluster_traj(gmx_executable, inputs, grps, method='linkage', cutoff=0.1, suf
         gmx_executable, 'trjconv',
         '-f', inputs['traj'],
         '-s', inputs['config'],
+        '-n', inputs['index'],
         '-o', outputs['nojump'],
         '-center', 'yes',
         '-pbc', 'nojump',
-        '-drop', inputs['xvg'],
-        '-dropover', '0'
     ]
-    if inputs['index'] is not None:
-        args.extend(['-n', inputs['index']])
+
+    if coupled_only:
+        if inputs['xvg'] is None:
+            raise ValueError('The parameter "coupled_only" is set to True but no XVG file is provided.')
+        args.extend([
+            '-drop', inputs['xvg'],
+            '-dropover', '0'
+        ])
+
     returncode, stdout, stderr = run_gmx_cmd(args, prompt_input=f'{grps["center"]}\n{grps["output"]}\n')
     if returncode != 0:
         print(f'Error with return code: {returncode}):\n{stderr}')
@@ -78,13 +103,12 @@ def cluster_traj(gmx_executable, inputs, grps, method='linkage', cutoff=0.1, suf
         gmx_executable, 'trjconv',
         '-f', outputs['nojump'],
         '-s', inputs['config'],
+        '-n', inputs['index'],
         '-o', outputs['center'],
         '-center', 'yes',
         '-pbc', 'mol',
         '-ur', 'compact',
     ]
-    if inputs['index'] is not None:
-        args.extend(['-n', inputs['index']])
     returncode, stdout, stderr = run_gmx_cmd(args, prompt_input=f'{grps["center"]}\n{grps["output"]}\n')
     if returncode != 0:
         print(f'Error with return code: {returncode}):\n{stderr}')
@@ -94,6 +118,7 @@ def cluster_traj(gmx_executable, inputs, grps, method='linkage', cutoff=0.1, suf
         gmx_executable, 'cluster',
         '-f', outputs['center'],
         '-s', inputs['config'],
+        '-n', inputs['index'],
         '-o', outputs['rmsd-clust'],
         '-dist', outputs['rmsd-dist'],
         '-g', outputs['cluster-log'],
@@ -101,8 +126,6 @@ def cluster_traj(gmx_executable, inputs, grps, method='linkage', cutoff=0.1, suf
         '-cutoff', str(cutoff),
         '-method', method,
     ]
-    if inputs['index'] is not None:
-        args.extend(['-n', inputs['index']])
     returncode, stdout, stderr = run_gmx_cmd(args, prompt_input=f'{grps["rmsd"]}\n{grps["output"]}\n')
     if returncode != 0:
         print(f'Error with return code: {returncode}):\n{stderr}')