diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 45698d2214..788989a68f 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -575,7 +575,16 @@ if(PKG_USER-PLUMED)
   validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
   string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
-  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
   if(DOWNLOAD_PLUMED)
     if(BUILD_MPI)
       set(PLUMED_CONFIG_MPI "--enable-mpi")
@@ -620,7 +629,7 @@ if(PKG_USER-PLUMED)
     set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED plumed REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
@@ -654,7 +663,13 @@ if(PKG_USER-NETCDF)
 endif()
 
 if(PKG_USER-SMD)
-  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
+  find_package(Eigen3 NO_MODULE)
+  if(EIGEN3_FOUND)
+    set(DOWNLOAD_EIGEN3_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_EIGEN3_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
   if(DOWNLOAD_EIGEN3)
     message(STATUS "Eigen3 download requested - we will build our own")
     include(ExternalProject)
@@ -767,7 +782,13 @@ endif()
 
 if(PKG_MSCG)
   find_package(GSL REQUIRED)
-  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)
+  find_package(MSCG QUIET)
+  if(MSGC_FOUND)
+    set(DOWNLOAD_MSCG_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_MSCG_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
   if(DOWNLOAD_MSCG)
     if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
       message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")