Once installed, this directory contains CMakelist.txt, Makefile.pkg and a small program that you could use as a template when writing your own analysis software. Further explanation for the template code can be found in the Doxygen documentation (link to the latest development version): The CMakelist.txt can be used together with cmake to build the template program: $ source /path/to/GMXRC $ cmake /path/to/template Alternatively, setting CMAKE_PREFIX_PATH will direct cmake to find a particular GROMACS installation. The Makefile.pkg can be used if cmake is unavailable. It makes use of pkg-config to build the template program: $ source /path/to/GMXRC $ make -f Makefile.pkg You will need to make sure that you use a sufficiently similar C++ compiler and C++ Standard Library as the one that was used for compiling GROMACS, preferably the same one. Boost headers used to compile GROMACS are also required, and are automatically added to the include path by both of the above build systems. See the Doxygen documentation for using GROMACS as a library for more details about the build system used to build the template, as well as its limitations (link to the latest development version): ---------------------------------------------------------- If you are reading this in the distribution directory, remember that CMakelist.txt.template will be renamed to CMakelist.txt during the installation.