/usr/include/gromacs/thread_mpi/atomic/ is in gromacs-dev 4.6.5-1build1.
This file is owned by root:root, with mode 0o755.
..
/usr/include/gromacs/thread_mpi/atomic/cycles.h
/usr/include/gromacs/thread_mpi/atomic/derived.h
/usr/include/gromacs/thread_mpi/atomic/fujitsu_sparc64.h
/usr/include/gromacs/thread_mpi/atomic/gcc.h
/usr/include/gromacs/thread_mpi/atomic/gcc_ia64.h
/usr/include/gromacs/thread_mpi/atomic/gcc_intrinsics.h
/usr/include/gromacs/thread_mpi/atomic/gcc_ppc.h
/usr/include/gromacs/thread_mpi/atomic/gcc_spinlock.h
/usr/include/gromacs/thread_mpi/atomic/gcc_x86.h
/usr/include/gromacs/thread_mpi/atomic/msvc.h
/usr/include/gromacs/thread_mpi/atomic/suncc-sparc.h
/usr/include/gromacs/thread_mpi/atomic/xlc_ppc.h