From a0f22237e7bc7518b12ea3163bf13c49bce77454 Mon Sep 17 00:00:00 2001
From: Shreya Bhakat <your-email@example.com>
Date: Sun, 22 Feb 2026 16:37:20 +0000
Subject: [PATCH] Fix #5100: Auto-switch to non-linear MSD for custom frames

---
 package/MDAnalysis/analysis/msd.py | 32 ++++++++++++++----------------
 1 file changed, 15 insertions(+), 17 deletions(-)

diff --git a/package/MDAnalysis/analysis/msd.py b/package/MDAnalysis/analysis/msd.py
index 814ea37bed..49c86d5a31 100644
--- a/package/MDAnalysis/analysis/msd.py
+++ b/package/MDAnalysis/analysis/msd.py
@@ -64,26 +64,26 @@
 
 .. warning::
    To correctly compute the MSD using this analysis module, you must supply
-   coordinates in the **unwrapped** convention, also known as **no-jump**. 
-   That is, when atoms pass the periodic boundary, they must not be wrapped 
+   coordinates in the **unwrapped** convention, also known as **no-jump**.
+   That is, when atoms pass the periodic boundary, they must not be wrapped
    back into the primary simulation cell.
-   
-   In MDAnalysis you can use the 
+
+   In MDAnalysis you can use the
    :class:`~MDAnalysis.transformations.nojump.NoJump`
    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
       u.trajectory.add_transformations(NoJump(u))
-       
+
       # 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")
@@ -94,11 +94,11 @@
    dimensions must be defined before applying ``NoJump``, which can
    be accomplished by applying the
    :class:`~MDAnalysis.transformations.boxdimensions.set_dimensions`
-   transformation *before* the 
+   transformation *before* the
    :class:`~MDAnalysis.transformations.nojump.NoJump` transformation.
-   
+
    This replaces the need to preprocess trajectories externally.
-   
+
    In GROMACS, for example, this can be done using `gmx trjconv`_ with the
    ``-pbc nojump`` flag.
 
@@ -427,7 +427,7 @@ def _single_frame(self):
         ]
 
     def _conclude(self):
-        if self.non_linear:
+        if self.non_linear or (self.frames is not None and not self.fft):
             self._conclude_non_linear()
         else:
             if self.fft:
@@ -457,8 +457,7 @@ def _conclude_fft(self):  # with FFT, np.float64 bit prescision required.
         try:
             import tidynamics
         except ImportError:
-            raise ImportError(
-                """ERROR --- tidynamics was not found!
+            raise ImportError("""ERROR --- tidynamics was not found!
 
                 tidynamics is required to compute an FFT based MSD (default)
 
@@ -466,8 +465,7 @@ def _conclude_fft(self):  # with FFT, np.float64 bit prescision required.
 
                     pip install tidynamics
 
-                or set fft=False"""
-            )
+                or set fft=False""")
 
         positions = self._position_array.astype(np.float64)
         for n in ProgressBar(