diff --git a/flare/ase/otf.py b/flare/ase/otf.py
index d164477ce..33feb3e63 100644
--- a/flare/ase/otf.py
+++ b/flare/ase/otf.py
@@ -144,10 +144,11 @@ def md_step(self):
         Get new position in molecular dynamics based on the forces predicted by
         FLARE_Calculator or DFT calculator
         '''
-        pos = np.copy(self.structure.positions)
         self.md.step()
-        self.structure.positions = pos
-        return self.atoms.positions
+
+        # Return a copy so that future updates to atoms.positions doesn't also
+        # update structure.positions.
+        return np.copy(self.atoms.positions)
 
     # TODO: fix the temperature output in the log file
 
diff --git a/flare/otf.py b/flare/otf.py
index 6ce120d9c..a4628bdae 100644
--- a/flare/otf.py
+++ b/flare/otf.py
@@ -213,13 +213,7 @@ def run(self):
                 # compute forces and stds with GP
                 self.dft_step = False
                 self.compute_properties()
-                # print('positions pre:')
-                # print(self.structure.positions)
                 new_pos = self.md_step()
-                # print('positions post:')
-                # print(self.structure.positions)
-                # print('new pos:')
-                # print(new_pos)
 
                 # get max uncertainty atoms
                 std_in_bound, target_atoms = \
@@ -239,8 +233,6 @@ def run(self):
                     dft_frcs = deepcopy(self.structure.forces)
 
                     # run MD step & record the state
-                    # new_pos = self.md_step()
-                    # self.update_temperature(new_pos)
                     self.record_state()
 
                     # compute mae and write to output