diff --git a/source/gmx/CMakeLists.txt b/source/gmx/CMakeLists.txt
index 8fde1e6ab8..af78bc97f1 100644
--- a/source/gmx/CMakeLists.txt
+++ b/source/gmx/CMakeLists.txt
@@ -1,3 +1,7 @@
+message(
+  DEPRECATION
+    "The GROMACS plugin is deprecated and will be removed in a future version. "
+    "See https://arxiv.org/abs/2602.02234 for a third-party alternative.")
 message(STATUS "Build GROMACS plugin")
 
 file(GLOB PATCH_VERSIONS patches/*)
diff --git a/source/gmx/dp_gmx_patch b/source/gmx/dp_gmx_patch
index 8df3f12cc6..1c45477f77 100644
--- a/source/gmx/dp_gmx_patch
+++ b/source/gmx/dp_gmx_patch
@@ -1,4 +1,6 @@
 #!/bin/bash
+echo "WARNING: The GROMACS patch in deepmd-kit is deprecated and will be removed in a future version." >&2
+echo "WARNING: See https://arxiv.org/abs/2602.02234 for a third-party alternative." >&2
 DEEPMD_PATCH_SCRIPT_DIR=$(dirname $(readlink -f "$0"))
 DEEPMD_PATCH_ROOT=${DEEPMD_PATCH_SCRIPT_DIR}/../share/deepmd_gromacs_patches
 VERSION="NULL"