diff --git a/benchmarks/benchmarks/analysis/rms.py b/benchmarks/benchmarks/analysis/rms.py
index 3d34f386c5a..41517b78aa8 100644
--- a/benchmarks/benchmarks/analysis/rms.py
+++ b/benchmarks/benchmarks/analysis/rms.py
@@ -34,9 +34,9 @@ def setup(self, num_atoms, weights, center, superposition):
             self.u.trajectory[-1]
             self.B = self.u.atoms.positions.copy()[:num_atoms]
         except:
-            self.A = self.u.atoms.coordinates().copy()[:num_atoms]
+            self.A = self.u.atoms.positions().copy()[:num_atoms]
             self.u.trajectory[-1]
-            self.B = self.u.atoms.coordinates().copy()[:num_atoms]
+            self.B = self.u.atoms.positions().copy()[:num_atoms]
 
     def time_rmsd(self, num_atoms, weights, center, superposition):
         """Benchmark rmsd function using a setup similar to
diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py
index 352d934f9d5..25568ba6bf3 100644
--- a/package/MDAnalysis/analysis/encore/covariance.py
+++ b/package/MDAnalysis/analysis/encore/covariance.py
@@ -215,7 +215,7 @@ def covariance_matrix(ensemble,
         # Select the same atoms in reference structure
         reference_atom_selection = reference.select_atoms(
             ensemble.get_atom_selection_string())
-        reference_coordinates = reference_atom_selection.atoms.coordinates()
+        reference_coordinates = reference_atom_selection.atoms.positions()
 
         # Flatten reference coordinates
         reference_coordinates = reference_coordinates.flatten()
diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py
index 9e77df6f486..d8f6123216d 100644
--- a/package/MDAnalysis/units.py
+++ b/package/MDAnalysis/units.py
@@ -238,7 +238,8 @@
 timeUnit_factor = {
     'ps': 1.0, 'picosecond': 1.0,  # 1/1.0
     'fs': 1e3, 'femtosecond': 1e3,  # 1/1e-3,
-    'ns': 1e-3, 'nanosecond': 1e-3,  # 1/1e3,
+    'ns': 1e-9, 'nanosecond': 1e-9,  # 1/1e9,
+    'ms': 1e-3, 'millisecond': 1e-3,  # 1/1e3,
     'second': 1e-12, 'sec': 1e-12, 's': 1e-12,  # 1/1e12,
     'AKMA': 1 / 4.888821e-2,
 }