GROMACS

In the current method of initializing the GMX_*_LIBRARIES variables in the main CMakeLists.txt, the set() command will ignore cache variables of the same name. Since GMX_EXTRA_LIBRARIES, GMX_COMMON_LIBRARIES, and GMX_PUBLIC_LIBRARIES are initialized to "" with a local set() command, any customization of the libraries through cache variables or compilation flags (e.g. -DGMX_COMMON_LIBRARIES=library.so) is ignored.

By simply initializing the variables to their "original" values (even if nonexistent) will still allow for appending later, without ignoring cache variables.(e.g. set(GMX_EXTRA_LIBRARIES "${GMX_EXTRA_VARIABLES}"))