diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index d0a0ad7773e5723320c2369fda73754d386a3b57..5e6924684dee982b74cbd24858ed130a04b7c74b 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -354,7 +354,7 @@ void PCAVars::unlockRequests() {
 
 void PCAVars::calculate() {
 
-  if(!nopbc) makeWhole();
+  if(!nopbc && getNumberOfAtoms()>0) makeWhole();
 
   // Clear the reference value pack
   mypack.clear();