debian specific patch information for gromacs / 4.5.5-2

 CMakeLists.txt                                                    |   88 
 COPYING-OTHER                                                     |   83 
 Makefile.am                                                       |    1 
 admin/GerritBuild.bat                                             |    3 
 cmake/CMakeASM-NASMInformation.cmake                              |   30 
 cmake/CMakeASM_NASMInformation.cmake                              |   30 
 cmake/CMakeDetermineASM-NASMCompiler.cmake                        |   13 
 cmake/CMakeDetermineASM_NASMCompiler.cmake                        |   13 
 cmake/CMakeTestASM-NASMCompiler.cmake                             |    9 
 cmake/CMakeTestASM_NASMCompiler.cmake                             |    9 
 cmake/FindLAPACK.cmake                                            |    2 
 cmake/ThreadMPI.cmake                                             |   11 
 cmake/Toolchain-BlueGeneP.cmake                                   |    8 
 cmake/gmxCFlags.cmake                                             |   38 
 cmake/gmxGenerateVersionInfo.cmake                                |  221 -
 cmake/gmxTestIsfinite.cmake                                       |   77 
 include/checkpoint.h                                              |    6 
 include/domdec.h                                                  |    7 
 include/domdec_network.h                                          |    7 
 include/gstat.h                                                   |    6 
 include/maths.h                                                   |   10 
 include/mdrun.h                                                   |    6 
 include/mtxio.h                                                   |    2 
 include/thread_mpi/atomic/gcc_x86.h                               |   37 
 include/thread_mpi/numa_malloc.h                                  |    2 
 include/types/commrec.h                                           |    3 
 include/types/simple.h                                            |    4 
 include/vsite.h                                                   |   13 
 share/html/online/mdp_opt.html                                    |  176 
 share/html/online/xpm.html                                        |    2 
 share/top/charmm27.ff/ions.itp                                    |    2 
 src/config.h.cmakein                                              |    6 
 src/gmxlib/CMakeLists.txt                                         |   18 
 src/gmxlib/atomprop.c                                             |   12 
 src/gmxlib/checkpoint.c                                           |   63 
 src/gmxlib/enxio.c                                                |   14 
 src/gmxlib/futil.c                                                |   38 
 src/gmxlib/gmx_lapack/dlasq2.c                                    |    4 
 src/gmxlib/gmx_lapack/slasq2.c                                    |    4 
 src/gmxlib/gmxfio.c                                               |    2 
 src/gmxlib/libxdrf.c                                              |    2 
 src/gmxlib/maths.c                                                |   65 
 src/gmxlib/mshift.c                                               |    2 
 src/gmxlib/mtxio.c                                                |    4 
 src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h  |   31 
 src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w3_bluegene.h   |   15 
 src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w3w3_bluegene.h |   15 
 src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w4_bluegene.h   |   15 
 src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w4w4_bluegene.h |   15 
 src/gmxlib/rmpbc.c                                                |    6 
 src/gmxlib/selection/params.c                                     |   12 
 src/gmxlib/selection/parser.c                                     |  314 -
 src/gmxlib/selection/parser.h                                     |    4 
 src/gmxlib/selection/scanner_internal.c                           |    2 
 src/gmxlib/shift_util.c                                           |    4 
 src/gmxlib/thread_mpi/numa_malloc.c                               |    2 
 src/gmxlib/thread_mpi/pthreads.c                                  |   55 
 src/gmxlib/tpxio.c                                                |    4 
 src/gmxlib/trajana/nbsearch.c                                     |    2 
 src/gmxlib/trajana/trajana.c                                      |    6 
 src/gmxlib/trnio.c                                                |    2 
 src/gmxlib/wman.c                                                 |  231 +
 src/kernel/gen_ad.c                                               |    6 
 src/kernel/gen_vsite.c                                            |    2 
 src/kernel/genhydro.c                                             |    2 
 src/kernel/gmxcheck.c                                             |    6 
 src/kernel/grompp.c                                               |   19 
 src/kernel/md.c                                                   |   27 
 src/kernel/md_openmm.c                                            |    3 
 src/kernel/mdrun.c                                                |    5 
 src/kernel/pdb2top.c                                              |  117 
 src/kernel/pgutil.c                                               |   64 
 src/kernel/pgutil.h                                               |    7 
 src/kernel/readir.c                                               |   24 
 src/kernel/resall.c                                               |    4 
 src/kernel/runner.c                                               |    3 
 src/kernel/tpbcmp.c                                               |    2 
 src/mdlib/CMakeLists.txt                                          |    4 
 src/mdlib/clincs.c                                                |   13 
 src/mdlib/constr.c                                                |    4 
 src/mdlib/coupling.c                                              |    7 
 src/mdlib/domdec.c                                                |    5 
 src/mdlib/domdec_setup.c                                          |    2 
 src/mdlib/ebin.c                                                  |    2 
 src/mdlib/fft5d.c                                                 |    8 
 src/mdlib/fftpack.c                                               | 1570 ++++++++
 src/mdlib/fftpack.h                                               |   56 
 src/mdlib/genborn.c                                               |    2 
 src/mdlib/gmx_fft_fftpack.c                                       | 1765 ----------
 src/mdlib/gmx_fft_fftw3.c                                         |    3 
 src/mdlib/md_support.c                                            |   37 
 src/mdlib/mdebin_bar.c                                            |    4 
 src/mdlib/minimize.c                                              |   32 
 src/mdlib/pme.c                                                   |   10 
 src/mdlib/pull.c                                                  |    6 
 src/mdlib/shellfc.c                                               |   51 
 src/mdlib/sim_util.c                                              |   41 
 src/mdlib/stat.c                                                  |   63 
 src/mdlib/vsite.c                                                 |  153 
 src/tools/anadih.c                                                |   18 
 src/tools/autocorr.c                                              |    2 
 src/tools/do_dssp.c                                               |   38 
 src/tools/g_sigeps.c                                              |   12 
 src/tools/geminate.c                                              |    8 
 src/tools/gmx_anaeig.c                                            |   40 
 src/tools/gmx_analyze.c                                           |   36 
 src/tools/gmx_angle.c                                             |   20 
 src/tools/gmx_bar.c                                               |    6 
 src/tools/gmx_bond.c                                              |    2 
 src/tools/gmx_chi.c                                               |   18 
 src/tools/gmx_cluster.c                                           |   10 
 src/tools/gmx_clustsize.c                                         |    2 
 src/tools/gmx_current.c                                           |    4 
 src/tools/gmx_density.c                                           |   12 
 src/tools/gmx_dielectric.c                                        |    6 
 src/tools/gmx_dipoles.c                                           |   12 
 src/tools/gmx_dist.c                                              |    4 
 src/tools/gmx_editconf.c                                          |   17 
 src/tools/gmx_enemat.c                                            |    2 
 src/tools/gmx_energy.c                                            |   19 
 src/tools/gmx_genbox.c                                            |   16 
 src/tools/gmx_genpr.c                                             |    4 
 src/tools/gmx_gyrate.c                                            |    2 
 src/tools/gmx_h2order.c                                           |    2 
 src/tools/gmx_helix.c                                             |    2 
 src/tools/gmx_kinetics.c                                          |    2 
 src/tools/gmx_mdmat.c                                             |    2 
 src/tools/gmx_membed.c                                            |    8 
 src/tools/gmx_mindist.c                                           |    2 
 src/tools/gmx_morph.c                                             |   10 
 src/tools/gmx_msd.c                                               |    4 
 src/tools/gmx_nmtraj.c                                            |    2 
 src/tools/gmx_order.c                                             |    2 
 src/tools/gmx_potential.c                                         |    8 
 src/tools/gmx_rmsdist.c                                           |    4 
 src/tools/gmx_saltbr.c                                            |    2 
 src/tools/gmx_select.c                                            |    3 
 src/tools/gmx_sham.c                                              |  269 +
 src/tools/gmx_sorient.c                                           |   12 
 src/tools/gmx_spatial.c                                           |    2 
 src/tools/gmx_tcaf.c                                              |   24 
 src/tools/gmx_trjconv.c                                           |    6 
 src/tools/gmx_tune_pme.c                                          |   72 
 src/tools/gmx_vanhove.c                                           |    8 
 src/tools/gmx_velacc.c                                            |    6 
 src/tools/gmx_wheel.c                                             |    2 
 src/tools/hxprops.c                                               |    6 
 src/tools/mk_angndx.c                                             |    2 
 148 files changed, 3880 insertions(+), 2909 deletions(-)

 README |    9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

 man/man1/g_analyze.1  |    2 +-
 man/man1/g_dist.1     |    2 +-
 man/man1/g_hydorder.1 |    2 +-
 man/man1/g_mindist.1  |    2 +-
 man/man1/g_tune_pme.1 |    2 +-
 man/man1/g_wham.1     |    2 +-
 src/kernel/hizzie.c   |    2 +-
 src/kernel/readir.c   |    2 +-
 src/tools/gmx_genpr.c |    2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)