diff --git a/dpgen/generator/run.py b/dpgen/generator/run.py
index 0ce513a96..5190d91f9 100644
--- a/dpgen/generator/run.py
+++ b/dpgen/generator/run.py
@@ -2436,6 +2436,13 @@ def _read_model_devi_file(
                     )
                     os.rename(traj_files_sorted[ibead][itraj], new_filename)
     model_devi = np.loadtxt(os.path.join(task_path, "model_devi.out"))
+    if model_devi.ndim == 2:
+        # Some LAMMPS fixes evaluate a model repeatedly at the same timestep.
+        # The final evaluation describes the accepted configuration that is
+        # written to the trajectory, so discard earlier intermediate rows.
+        _, reverse_indices = np.unique(model_devi[::-1, 0], return_index=True)
+        last_indices = model_devi.shape[0] - 1 - reverse_indices
+        model_devi = model_devi[np.sort(last_indices)]
     if model_devi_f_avg_relative:
         if model_devi_merge_traj is True:
             all_traj = os.path.join(task_path, "all.lammpstrj")
diff --git a/tests/generator/test_make_md.py b/tests/generator/test_make_md.py
index ab36225cc..b1f3e9c21 100644
--- a/tests/generator/test_make_md.py
+++ b/tests/generator/test_make_md.py
@@ -312,6 +312,25 @@ def test_read_model_devi_file_pimd(self):
                 os.path.isfile(os.path.join(path, f"traj/{istep}.lammpstrj"))
             )
 
+    def test_read_model_devi_file_keeps_last_row_per_timestep(self):
+        """Intermediate model evaluations must not select stale structures."""
+        with tempfile.TemporaryDirectory() as task_path:
+            model_devi = np.array(
+                [
+                    [0, 0.01, 0, 0, 0.02, 0, 0],
+                    [10, 0.03, 0, 0, 0.04, 0, 0],
+                    [10, 0.05, 0, 0, 0.06, 0, 0],
+                    [20, 0.07, 0, 0, 0.08, 0, 0],
+                    [20, 0.09, 0, 0, 0.10, 0, 0],
+                    [20, 0.11, 0, 0, 0.12, 0, 0],
+                ]
+            )
+            np.savetxt(os.path.join(task_path, "model_devi.out"), model_devi)
+
+            result = _read_model_devi_file(task_path)
+
+        np.testing.assert_array_equal(result, model_devi[[0, 2, 5]])
+
 
 class TestMakeModelDeviRevMat(unittest.TestCase):
     def tearDown(self):