From 55f601c309dfd8fdedb1112124315be0c2e320f5 Mon Sep 17 00:00:00 2001
From: DhanushkaWeerakoon
 <34727025+DhanushkaWeerakoon@users.noreply.github.com>
Date: Wed, 22 Apr 2026 14:28:55 +0100
Subject: [PATCH 1/2] Changed definition of self._groupselections_ref_coords64
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Changed self.reference.select_atoms(…) (line 736) to
self.reference.universe.select_atoms(…)
---
 package/CHANGELOG                  | 4 +++-
 package/MDAnalysis/analysis/rms.py | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index ca30fcb440..499baee788 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -17,11 +17,13 @@ The rules for this file:
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
-         ollyfutur, Amarendra22, charity-g
+         ollyfutur, Amarendra22, charity-g, DhanushkaWeerakoon
 
  * 2.11.0
 
 Fixes
+ * Fix mismatch in target and reference groupselection coordinates which
+   can occur during RMSD calculations (Issue #2797) 
  * `MDAnalysis.analysis.atomicdistances.AtomicDistances` results are now
    consistent with expected `analysis` documentation data type = Results
    (Issue #4819, PR #5347)
diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py
index 4b76723e7b..54dac2c0ff 100644
--- a/package/MDAnalysis/analysis/rms.py
+++ b/package/MDAnalysis/analysis/rms.py
@@ -733,7 +733,7 @@ def _prepare(self):
             if self._groupselections_atoms:
                 self._groupselections_ref_coords64 = [
                     (
-                        self.reference.select_atoms(
+                        self.reference.universe.select_atoms(
                             *s["reference"]
                         ).positions.astype(np.float64)
                     )

From 03fb4b5f9a6d09a0a7579cf2823e54845c3b63cc Mon Sep 17 00:00:00 2001
From: DhanushkaWeerakoon
 <34727025+DhanushkaWeerakoon@users.noreply.github.com>
Date: Wed, 22 Apr 2026 14:53:27 +0100
Subject: [PATCH 2/2] Added name to AUTHORS list

---
 package/AUTHORS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/package/AUTHORS b/package/AUTHORS
index e8e41573d9..4cd9d75a3a 100644
--- a/package/AUTHORS
+++ b/package/AUTHORS
@@ -280,6 +280,7 @@ Chronological list of authors
   - Amarendra Mohan
   - Shubham Mittal  
   - Charity Grey
+  - Dhanushka Weerakoon
 
 External code
 -------------