Added NoJump on-the-fly example to MSD documentation (Issue #4169)

example/msd_nojump_demo.py

@@ -0,0 +1,48 @@
+# mypy: ignore-errors
+import MDAnalysis as mda
+from MDAnalysis.analysis.msd import EinsteinMSD
+from MDAnalysis.tests.datafiles import RANDOM_WALK, RANDOM_WALK_TOPO
+from MDAnalysis.transformations import NoJump
+import matplotlib.pyplot as plt
+
+print("Using input files:")
+print("Topology:", RANDOM_WALK_TOPO)
+print("Trajectory:", RANDOM_WALK)
+
+u = mda.Universe(RANDOM_WALK_TOPO, RANDOM_WALK)
+
+# --- FIX: define box dimensions BEFORE NoJump runs ---
+box = [100.0, 100.0, 100.0, 90.0, 90.0, 90.0]
+
+
+def set_box(ts):
+    ts.dimensions = box
+    return ts
+
+
+# Apply transformations in correct order
+u.trajectory.add_transformations(
+    set_box,  # must come first
+    NoJump(u),  # requires PBC
+)
+
+# Compute MSD
+msd = EinsteinMSD(u, select="all", msd_type="xyz", fft=False)
+msd.run()
+
+lagtimes = msd.results.delta_t_values
+msd_values = msd.results.timeseries
+
+plt.figure(figsize=(6, 4))
+plt.plot(lagtimes, msd_values, label="Computed MSD")
+plt.plot(lagtimes, 6 * lagtimes, "--", label="Theoretical 3D MSD (6τ)")
+plt.xlabel("Lag time (τ)")
+plt.ylabel("MSD")
+plt.legend()
+plt.title("Mean Squared Displacement with NoJump")
+
+plt.savefig("example/msd_nojump.png", dpi=150, bbox_inches="tight")
+
+plt.close()
+
+print("Saved plot to msd_nojump.png")

package/AUTHORS

@@ -265,6 +265,7 @@ Chronological list of authors
   - Raúl Lois-Cuns  
   - Pranay Pelapkar
   - Shreejan Dolai
+  - Tanisha Dubey 
 
 External code
 -------------

package/MDAnalysis/analysis/msd.py

@@ -69,8 +69,33 @@
    back into the primary simulation cell.
 
    In MDAnalysis you can use the 
-   :class:`~MDAnalysis.transformations.nojump.NoJump`
-   transformation. 
+    :class:`~MDAnalysis.transformations.nojump.NoJump`
+    transformation. 
+    transformation to unwrap coordinates on-the-fly.
+
+    A minimal example:
+
+    .. code-block:: python
+
+        import MDAnalysis as mda
+        from MDAnalysis.transformations import NoJump
+
+        u = mda.Universe(TOP, TRAJ)
+
+        # Apply NoJump transformation to unwrap coordinates
+        nojump = NoJump(u)
+        u.trajectory.add_transformations(nojump)
+
+        # Now the trajectory is unwrapped and MSD can be computed normally:
+        from MDAnalysis.analysis.msd import EinsteinMSD
+        MSD = EinsteinMSD(u, select="all", msd_type="xyz")
+        MSD.run()
+
+   This example assumes that the trajectory contains periodic box
+   dimensions. If no periodic boundary information is present, box
+   dimensions must be defined before applying ``NoJump``.
+
+   This replaces the need to preprocess trajectories externally.
 
    In GROMACS, for example, this can be done using `gmx trjconv`_ with the
    ``-pbc nojump`` flag.