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/usr/include/gromacs/gmx_header_config.h is in gromacs-dev 4.6.5-1build1.

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/* This include file will be configured by CMake and
 * installed with GROMACS header files so that they can
 * refer to a central location for #defines that will be
 * available for builds of projects that depend on GROMACS.
 */

/* Detect Cygwin */
/* #undef GMX_CYGWIN */

/* Detect native (i.e. non-Cygwin) Windows */
/* #undef GMX_NATIVE_WINDOWS */