diff --git a/src/generic/FitToTemplate.cpp b/src/generic/FitToTemplate.cpp
index b227be8a1aa4f8deaa7bdfacab5dfde37ac95298..962c2ea514005a33886e33f9bbd23b938d5df6b5 100644
--- a/src/generic/FitToTemplate.cpp
+++ b/src/generic/FitToTemplate.cpp
@@ -77,6 +77,11 @@ As a general rule, put it at the top of the input file. Also, unless you
 know exactly what you are doing, leave the default stride (1), so that
 this action is performed at every MD step.
 
+\warning
+The molecule used for alignment should be whole.
+In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref FIT_TO_TEMPLATE .
+
+
 \par Examples
 
 Align the atomic position to a template then print them.