7 files changed, 291 insertions, 370 deletions

diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index 7d849d75ed40..af2158243ac5 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -2,198 +2,139 @@
 # $FreeBSD$
 
 PORTNAME=	gromacs
-PORTVERSION=	4.5.5
-PORTREVISION=	1
+PORTVERSION=	4.6
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Compute molecular dynamics
 
-USE_GNOME=	libxml2
-USE_GMAKE=	yes
-USE_AUTOTOOLS=	libtool
-USE_LDCONFIG=	yes
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
-CONFIGURE_ARGS=	--exec-prefix=${PREFIX} --program-suffix="" --enable-shared
-
-PLIST_SUB=	BUILD=${MACHINE_ARCH}-portbld-freebsd${OSREL}
-
-OPTIONS_DEFINE= FFTW GSL FLOAT X11 MPI
-OPTIONS_DEFAULT= FFTW FFTW3 GSL X11
-OPTIONS_SINGLE=	FFTW MPI
-OPTIONS_SINGLE_FFTW=	FFTW2 FFTW3
-OPTIONS_SINGLE_MPI=	MPICH OMPI
-
-FFTW_DESC=	Use FFT routines
-FFTW2_DESC=	Use FFT routines from math/fftw
-FFTW3_DESC=	Use FFT routines from math/fftw3
-GSL_DESC=	Enable extra analysis using math/gsl
-FLOAT_DESC=	Use single instead of double precision
-MPI_DESC=	Enable MPI support
-MPICH_DESC=	Enable MPI support using net/mpich2
-OMPI_DESC=	Enable MPI support using net/openmpi
+LICENSE=	LGPL21
 
-.include <bsd.port.pre.mk>
+OPTIONS_DEFINE=	ATLAS FLOAT GSL SIMD X11
+OPTIONS_DEFAULT=	FLOAT GSL X11
+OPTIONS_RADIO=	MPI
+OPTIONS_RADIO_MPI=	MPICH OMPI
 
-.if ${ARCH} == i386
-CONFIGURE_ARGS+=	--disable-ia32-sse
+ATLAS_DESC=	Use ATLAS for BLAS and LAPACK
+FLOAT_DESC=	Use single instead of double precision
+GSL_DESC=	Extra analysis using math/gsl
+MPICH_DESC=	MPI support using net/mpich2
+OMPI_DESC=	MPI support using net/openmpi
+
+USE_FORTRAN=	yes
+USE_PERL5=	yes
+USE_PKGCONFIG=	build
+USE_CMAKE=	yes
+CMAKE_ARGS=	-DBLAS_LIBRARIES:FILEPATH="${BLAS_LIBS}" \
+		-DLAPACK_LIBRARIES:FILEPATH="${LAPACK_LIBS}"
+USE_LDCONFIG=	yes
+MAKE_JOBS_SAFE=	yes
+
+MAN1=		do_dssp.1 editconf.1 eneconv.1 g_anadock.1 \
+		g_anaeig.1 g_analyze.1 g_angle.1 g_bar.1 \
+		g_bond.1 g_bundle.1 g_chi.1 g_cluster.1 \
+		g_clustsize.1 g_confrms.1 g_covar.1 g_current.1 \
+		g_density.1 g_densmap.1 g_densorder.1 g_dielectric.1 \
+		g_dipoles.1 g_disre.1 g_dist.1 g_dos.1 \
+		g_dyecoupl.1 g_dyndom.1 g_enemat.1 g_energy.1 \
+		g_filter.1 g_gyrate.1 g_h2order.1 g_hbond.1 \
+		g_helix.1 g_helixorient.1 g_hydorder.1 g_kinetics.1 \
+		g_lie.1 g_mdmat.1 g_membed.1 g_mindist.1 \
+		g_morph.1 g_msd.1 g_nmeig.1 g_nmens.1 \
+		g_nmtraj.1 g_order.1 g_pme_error.1 g_polystat.1 \
+		g_potential.1 g_principal.1 g_protonate.1 g_rama.1 \
+		g_rdf.1 g_rms.1 g_rmsdist.1 g_rmsf.1 \
+		g_rotacf.1 g_rotmat.1 g_saltbr.1 g_sans.1 \
+		g_sas.1 g_select.1 g_sgangle.1 g_sham.1 \
+		g_sigeps.1 g_sorient.1 g_spatial.1 g_spol.1 \
+		g_tcaf.1 g_traj.1 g_tune_pme.1 g_vanhove.1 \
+		g_velacc.1 g_wham.1 g_wheel.1 g_x2top.1 \
+		genbox.1 genconf.1 genion.1 genrestr.1 \
+		gmxcheck.1 gmxdump.1 grompp.1 make_edi.1 \
+		make_ndx.1 mdrun.1 mk_angndx.1 pdb2gmx.1 \
+		tpbconv.1 trjcat.1 trjconv.1 trjorder.1 \
+		xpm2ps.1
+MAN7=		gromacs.7
+
+.include <bsd.port.options.mk>
+
+.if ${PORT_OPTIONS:MATLAS}
+LIB_DEPENDS+=	alapack:${PORTSDIR}/math/atlas
+BLAS_LIBS=	${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so
+LAPACK_LIBS=	${LOCALBASE}/lib/libalapack.so
+.else
+LIB_DEPENDS+=	blas:${PORTSDIR}/math/blas \
+		lapack:${PORTSDIR}/math/lapack
+BLAS_LIBS=	${LOCALBASE}/lib/libblas.so
+LAPACK_LIBS=	${LOCALBASE}/lib/liblapack.so
 .endif
 
-.if ${PORT_OPTIONS:MFFTW3}
-CONFIGURE_ARGS+=	--with-fft=fftw3
-. if ${PORT_OPTIONS:MFLOAT}
+.if ${PORT_OPTIONS:MFLOAT}
+BUILD_DEPENDS+=	fftw3>0:${PORTSDIR}/math/fftw3
 LIB_DEPENDS+=	fftw3f:${PORTSDIR}/math/fftw3-float
-. else
-LIB_DEPENDS+=	fftw3:${PORTSDIR}/math/fftw3
-. endif
+CMAKE_ARGS+=	-DGMX_DOUBLE:BOOL=OFF
+PLIST_SUB+=	SUFFIX_D=""
 .else
-. if ${PORT_OPTIONS:MFFTW2}
-CONFIGURE_ARGS+=	--with-fft=fftw2
-.  if ${PORT_OPTIONS:MFLOAT}
-LIB_DEPENDS+=	sfftw.2:${PORTSDIR}/math/fftw-float
-.  else
-LIB_DEPENDS+=	fftw.2:${PORTSDIR}/math/fftw
-.  endif
-. else
-CONFIGURE_ARGS+=	--with-fft=fftpack
-. endif
+LIB_DEPENDS+=	fftw3:${PORTSDIR}/math/fftw3
+CMAKE_ARGS+=	-DGMX_DOUBLE:BOOL=ON
+PLIST_SUB+=	SUFFIX_D="_d"
 .endif
 
 .if ${PORT_OPTIONS:MGSL}
-CONFIGURE_ARGS+=	--with-gsl
-LIB_DEPENDS+=	gsl.16:${PORTSDIR}/math/gsl
+LIB_DEPENDS+=	gsl:${PORTSDIR}/math/gsl
+CMAKE_ARGS+=	-DGMX_GSL:BOOL=ON
 .else
-CONFIGURE_ARGS+=	--without-gsl
+CMAKE_ARGS+=	-DGMX_GSL:BOOL=OFF
+.endif
+
+.if empty(PORT_OPTIONS:MSIMD)
+CMAKE_ARGS+=	-DGMX_CPU_ACCELERATION:STRING="None"
 .endif
 
 .if ${PORT_OPTIONS:MX11}
+USE_XORG=	xext x11
+CMAKE_ARGS+=	-DGMX_X11:BOOL=ON
 PLIST_SUB+=	X11=""
-CONFIGURE_ARGS+=	--with-x
-USE_XORG=	x11
+MAN1+=		g_xrama.1 ngmx.1
 .else
+CMAKE_ARGS+=	-DGMX_X11:BOOL=OFF
 PLIST_SUB+=	X11="@comment "
-CONFIGURE_ARGS+=	--without-x
 .endif
 
-.if ${PORT_OPTIONS:MFLOAT}
-PLIST_SUB+=	SUFFIX_D="" SUFFIX_DOUBLE=""
+.if ${PORT_OPTIONS:MMPICH} || ${PORT_OPTIONS:MOMPI}
+CMAKE_ARGS+=	-DGMX_MPI:BOOL=ON \
+		-DMPI_C_COMPILER:FILEPATH="${MPICC}"
+PLIST_SUB+=	SUFFIX_MPI="_mpi"
 .else
-CONFIGURE_ARGS+=	--disable-float
-PLIST_SUB+=	SUFFIX_D=_d SUFFIX_DOUBLE=_double
+CMAKE_ARGS+=	-DGMX_MPI:BOOL=OFF
+PLIST_SUB+=	SUFFIX_MPI=""
 .endif
 
-.if ${PORT_OPTIONS:MMPICH} || ${PORT_OPTIONS:MOMPI}
-CONFIGURE_ARGS+=	--enable-mpi
 .if ${PORT_OPTIONS:MMPICH}
-CONFIGURE_ENV+=	MPICC=${PREFIX}/bin/mpicc
 BUILD_DEPENDS+=	${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2
 RUN_DEPENDS+=	${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2
-.elif ${PORT_OPTIONS:MOMPI}
-CONFIGURE_ENV+=	MPICC=${PREFIX}/mpi/openmpi/bin/mpicc
+MPICC=		${LOCALBASE}/bin/mpicc
+.endif
+
+.if ${PORT_OPTIONS:MOMPI}
 BUILD_DEPENDS+=	${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi
 RUN_DEPENDS+=	${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi
-.endif
-PLIST_SUB+=	SUFFIX_MPI="_mpi" MPI=""
-.else
-PLIST_SUB+=	SUFFIX_MPI="" MPI="@comment "
+MPICC=		${LOCALBASE}/mpi/openmpi/bin/mpicc
 .endif
 
-MAN1=	do_dssp.1 \
-	editconf.1 \
-	eneconv.1 \
-	g_anadock.1 \
-	g_anaeig.1 \
-	g_analyze.1 \
-	g_angle.1 \
-	g_bar.1 \
-	g_bond.1 \
-	g_bundle.1 \
-	g_chi.1 \
-	g_cluster.1 \
-	g_clustsize.1 \
-	g_confrms.1 \
-	g_covar.1 \
-	g_current.1 \
-	g_density.1 \
-	g_densmap.1 \
-	g_densorder.1 \
-	g_dielectric.1 \
-	g_dih.1 \
-	g_dipoles.1 \
-	g_disre.1 \
-	g_dist.1 \
-	g_dyndom.1 \
-	g_enemat.1 \
-	g_energy.1 \
-	g_filter.1 \
-	g_gyrate.1 \
-	g_h2order.1 \
-	g_hbond.1 \
-	g_helix.1 \
-	g_helixorient.1 \
-	g_hydorder.1 \
-	g_lie.1 \
-	g_mdmat.1 \
-	g_membed.1 \
-	g_mindist.1 \
-	g_morph.1 \
-	g_msd.1 \
-	g_nmeig.1 \
-	g_nmens.1 \
-	g_nmtraj.1 \
-	g_options.1 \
-	g_order.1 \
-	g_pme_error.1 \
-	g_polystat.1 \
-	g_potential.1 \
-	g_principal.1 \
-	g_protonate.1 \
-	g_rama.1 \
-	g_rdf.1 \
-	g_rms.1 \
-	g_rmsdist.1 \
-	g_rmsf.1 \
-	g_rotacf.1 \
-	g_rotmat.1 \
-	g_saltbr.1 \
-	g_sas.1 \
-	g_select.1 \
-	g_sgangle.1 \
-	g_sham.1 \
-	g_sigeps.1 \
-	g_sorient.1 \
-	g_spatial.1 \
-	g_spol.1 \
-	g_tcaf.1 \
-	g_traj.1 \
-	g_tune_pme.1 \
-	g_vanhove.1 \
-	g_velacc.1 \
-	g_wham.1 \
-	g_wheel.1 \
-	g_x2top.1 \
-	g_xrama.1 \
-	genbox.1 \
-	genconf.1 \
-	genion.1 \
-	genrestr.1 \
-	gmxcheck.1 \
-	gmxdump.1 \
-	grompp.1 \
-	make_edi.1 \
-	make_ndx.1 \
-	mdrun.1 \
-	mk_angndx.1 \
-	ngmx.1 \
-	pdb2gmx.1 \
-	tpbconv.1 \
-	trjcat.1 \
-	trjconv.1 \
-	trjorder.1 \
-	xpm2ps.1
-
-MAN7=	gromacs.7
-
-.include <bsd.port.post.mk>
+post-patch:
+	@${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \
+		${REINPLACE_CMD} -e \
+		's|share/man|man| ; \
+		 s|-lpthread|${PTHREAD_LIBS}| ; \
+		 /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|'
+	@${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \
+		's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \
+		 s|LDLIB}/pkgconfig|LDLIB}/../libdata/pkgconfig|'
+	@${FIND} ${WRKSRC} -name "*.pl" | ${XARGS} ${REINPLACE_CMD} -e \
+		's|/usr/bin/perl|${PERL}|'
+	@${FIND} ${WRKSRC} -name "*.sh" | ${XARGS} ${REINPLACE_CMD} -e \
+		's|/bin/bash|/bin/sh|'
+
+.include <bsd.port.mk>
diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo
index 0c0a907c3463..4f462ee9288e 100644
--- a/science/gromacs/distinfo
+++ b/science/gromacs/distinfo
@@ -1,2 +1,2 @@
-SHA256 (gromacs-4.5.5.tar.gz) = e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba
-SIZE (gromacs-4.5.5.tar.gz) = 10398178
+SHA256 (gromacs-4.6.tar.gz) = f695ea814b10cb9afa8d69241fed703c6e20156bab96ed4b25f817ad85a8dbde
+SIZE (gromacs-4.6.tar.gz) = 10098687
diff --git a/science/gromacs/files/patch-src__gmxlib__Makefile.in b/science/gromacs/files/patch-src__gmxlib__Makefile.in
deleted file mode 100644
index 4557deb050b7..000000000000
--- a/science/gromacs/files/patch-src__gmxlib__Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./src/gmxlib/Makefile.in.orig	2010-08-23 15:53:16.000000000 +0200
-+++ ./src/gmxlib/Makefile.in	2010-08-23 15:53:32.000000000 +0200
-@@ -365,7 +365,7 @@
- 	gmx_system_xdr.c md5.c vmdio.c vmddlopen.c sighandler.c oenv.c \
- 	gmxfio_rw.c gmxfio_asc.c gmxfio_bin.c gmxfio_xdr.c \
- 	$(am__append_1)
--pkgconfigdir = ${libdir}/pkgconfig
-+pkgconfigdir = ${PREFIX}/libdata/pkgconfig
- pkgconfig_DATA = libgmx@LIBSUFFIX@.pc
- 
- # clean all libtool libraries, since the target names might have changed
diff --git a/science/gromacs/files/patch-src__kernel__Makefile.in b/science/gromacs/files/patch-src__kernel__Makefile.in
deleted file mode 100644
index f135d2140e41..000000000000
--- a/science/gromacs/files/patch-src__kernel__Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./src/kernel/Makefile.in.orig	2010-08-23 15:52:04.000000000 +0200
-+++ ./src/kernel/Makefile.in	2010-08-23 15:53:01.000000000 +0200
-@@ -322,7 +322,7 @@
- top_srcdir = @top_srcdir@
- AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"
- lib_LTLIBRARIES = libgmxpreprocess@LIBSUFFIX@.la 
--pkgconfigdir = ${libdir}/pkgconfig
-+pkgconfigdir = ${PREFIX}/libdata/pkgconfig
- pkgconfig_DATA = libgmxpreprocess@LIBSUFFIX@.pc
- EXTRA_DIST = libgmxpreprocess.pc.cmakein
- LDADD = $(lib_LTLIBRARIES) ../mdlib/libmd@LIBSUFFIX@.la ../gmxlib/libgmx@LIBSUFFIX@.la 
diff --git a/science/gromacs/files/patch-src__mdlib__Makefile.in b/science/gromacs/files/patch-src__mdlib__Makefile.in
deleted file mode 100644
index 1b18a203fb3c..000000000000
--- a/science/gromacs/files/patch-src__mdlib__Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./src/mdlib/Makefile.in.orig	2010-08-23 15:53:46.000000000 +0200
-+++ ./src/mdlib/Makefile.in	2010-08-23 15:53:58.000000000 +0200
-@@ -262,7 +262,7 @@
- libmd@LIBSUFFIX@_la_DEPENDENCIES = ../gmxlib/libgmx@LIBSUFFIX@.la	
- libmd@LIBSUFFIX@_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@ $(FFT_LIBS) $(XML_LIBS) $(PTHREAD_LIBS)
- lib_LTLIBRARIES = libmd@LIBSUFFIX@.la
--pkgconfigdir = ${libdir}/pkgconfig
-+pkgconfigdir = ${PREFIX}/libdata/pkgconfig
- pkgconfig_DATA = libmd@LIBSUFFIX@.pc
- EXTRA_DIST = libmd.pc.cmakein
- libmd@LIBSUFFIX@_la_SOURCES = \
diff --git a/science/gromacs/files/patch-src__tools__Makefile.in b/science/gromacs/files/patch-src__tools__Makefile.in
deleted file mode 100644
index 5a2761b413f2..000000000000
--- a/science/gromacs/files/patch-src__tools__Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./src/tools/Makefile.in.orig	2010-08-23 15:51:50.000000000 +0200
-+++ ./src/tools/Makefile.in	2010-08-23 15:51:16.000000000 +0200
-@@ -726,7 +726,7 @@
- top_srcdir = @top_srcdir@
- AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"
- lib_LTLIBRARIES = libgmxana@LIBSUFFIX@.la
--pkgconfigdir = ${libdir}/pkgconfig
-+pkgconfigdir = ${PREFIX}/libdata/pkgconfig
- pkgconfig_DATA = libgmxana@LIBSUFFIX@.pc
- EXTRA_DIST = libgmxana.pc.cmakein
- libgmxana@LIBSUFFIX@_la_LIBADD = ../gmxlib/libgmx@LIBSUFFIX@.la	../mdlib/libmd@LIBSUFFIX@.la	
diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist
index 6d78a21ac208..09aa9094f735 100644
--- a/science/gromacs/pkg-plist
+++ b/science/gromacs/pkg-plist
@@ -6,104 +6,106 @@ bin/completion.bash
 bin/completion.csh
 bin/completion.zsh
 bin/demux.pl
-bin/do_dssp
-bin/editconf
-bin/eneconv
-bin/g_anadock
-bin/g_anaeig
-bin/g_analyze
-bin/g_angle
-bin/g_bar
-bin/g_bond
-bin/g_bundle
-bin/g_chi
-bin/g_cluster
-bin/g_clustsize
-bin/g_confrms
-bin/g_covar
-bin/g_current
-bin/g_density
-bin/g_densmap
-bin/g_densorder
-bin/g_dielectric
-bin/g_dih
-bin/g_dipoles
-bin/g_disre
-bin/g_dist
-bin/g_dos
-bin/g_dyndom
-bin/g_enemat
-bin/g_energy
-bin/g_filter
-bin/g_gyrate
-bin/g_h2order
-bin/g_hbond
-bin/g_helix
-bin/g_helixorient
-bin/g_hydorder
-bin/g_kinetics
-bin/g_lie
-bin/g_luck
-bin/g_mdmat
-bin/g_membed
-bin/g_mindist
-bin/g_morph
-bin/g_msd
-bin/g_nmeig
-bin/g_nmens
-bin/g_nmtraj
-bin/g_options
-bin/g_order
-bin/g_pme_error
-bin/g_polystat
-bin/g_potential
-bin/g_principal
-bin/g_protonate
-bin/g_rama
-bin/g_rdf
-bin/g_rms
-bin/g_rmsdist
-bin/g_rmsf
-bin/g_rotacf
-bin/g_rotmat
-bin/g_saltbr
-bin/g_sas
-bin/g_select
-bin/g_sgangle
-bin/g_sham
-bin/g_sigeps
-bin/g_sorient
-bin/g_spatial
-bin/g_spol
-bin/g_tcaf
-bin/g_traj
-bin/g_tune_pme
-bin/g_vanhove
-bin/g_velacc
-bin/g_wham
-bin/g_wheel
-bin/g_x2top
-%%X11%%bin/g_xrama
-bin/genbox
-bin/genconf
-bin/genion
-bin/genrestr
-bin/gmxcheck
-bin/gmxdump
-bin/grompp
-bin/make_edi
-bin/make_ndx
-bin/mdrun
-bin/mk_angndx
-%%X11%%bin/ngmx
-bin/pdb2gmx
-bin/tpbconv
-bin/trjcat
-bin/trjconv
-bin/trjorder
+bin/do_dssp%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/editconf%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/eneconv%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_anadock%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_anaeig%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_analyze%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_angle%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_bar%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_bond%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_bundle%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_chi%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_cluster%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_clustsize%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_confrms%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_covar%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_current%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_density%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_densmap%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_densorder%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_dielectric%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_dipoles%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_disre%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_dist%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_dos%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_dyecoupl%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_dyndom%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_enemat%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_energy%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_filter%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_gyrate%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_h2order%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_hbond%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_helix%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_helixorient%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_hydorder%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_kinetics%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_lie%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_luck%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_mdmat%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_membed%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_mindist%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_morph%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_msd%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_nmeig%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_nmens%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_nmtraj%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_options%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_order%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_pme_error%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_polystat%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_potential%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_principal%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_protonate%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_rama%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_rdf%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_rms%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_rmsdist%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_rmsf%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_rotacf%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_rotmat%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_saltbr%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_sans%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_sas%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_select%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_sgangle%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_sham%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_sigeps%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_sorient%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_spatial%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_spol%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_tcaf%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_traj%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_tune_pme%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_vanhove%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_velacc%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_wham%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_wheel%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/g_x2top%%SUFFIX_MPI%%%%SUFFIX_D%%
+%%X11%%bin/g_xrama%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/genbox%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/genconf%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/genion%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/genrestr%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/gmxcheck%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/gmxdump%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/grompp%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/make_edi%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/make_ndx%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/mdrun%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/mk_angndx%%SUFFIX_MPI%%%%SUFFIX_D%%
+%%X11%%bin/ngmx%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/pdb2gmx%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/tpbconv%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/trjcat%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/trjconv%%SUFFIX_MPI%%%%SUFFIX_D%%
+bin/trjorder%%SUFFIX_MPI%%%%SUFFIX_D%%
 bin/xplor2gmx.pl
-bin/xpm2ps
+bin/xpm2ps%%SUFFIX_MPI%%%%SUFFIX_D%%
 include/gromacs/3dview.h
+include/gromacs/CTestTestfile.cmake
 include/gromacs/assert.h
 include/gromacs/atomprop.h
 include/gromacs/bondf.h
@@ -117,7 +119,6 @@ include/gromacs/confio.h
 include/gromacs/constr.h
 include/gromacs/copyrite.h
 include/gromacs/coulomb.h
-include/gromacs/dihre.h
 include/gromacs/displacement.h
 include/gromacs/disre.h
 include/gromacs/do_fit.h
@@ -134,27 +135,48 @@ include/gromacs/gbutil.h
 include/gromacs/gen_ad.h
 include/gromacs/genborn.h
 include/gromacs/gmx_ana.h
-include/gromacs/gmx_arpack.h
-include/gromacs/gmx_blas.h
+include/gromacs/gmx_avx_double.h
+include/gromacs/gmx_avx_single.h
+include/gromacs/gmx_cpuid.h
 include/gromacs/gmx_cyclecounter.h
+include/gromacs/gmx_detect_hardware.h
 include/gromacs/gmx_fatal.h
+include/gromacs/gmx_fatal_collective.h
 include/gromacs/gmx_fft.h
 include/gromacs/gmx_ga2la.h
-include/gromacs/gmx_lapack.h
+include/gromacs/gmx_hash.h
+include/gromacs/gmx_header_config.h
+include/gromacs/gmx_math_x86_avx_128_fma_double.h
+include/gromacs/gmx_math_x86_avx_128_fma_single.h
+include/gromacs/gmx_math_x86_avx_256_double.h
+include/gromacs/gmx_math_x86_avx_256_single.h
+include/gromacs/gmx_math_x86_sse2_double.h
+include/gromacs/gmx_math_x86_sse2_single.h
+include/gromacs/gmx_math_x86_sse4_1_double.h
+include/gromacs/gmx_math_x86_sse4_1_single.h
 include/gromacs/gmx_matrix.h
+include/gromacs/gmx_omp.h
+include/gromacs/gmx_omp_nthreads.h
 include/gromacs/gmx_parallel_3dfft.h
 include/gromacs/gmx_random.h
+include/gromacs/gmx_simd_macros.h
 include/gromacs/gmx_sort.h
-include/gromacs/gmx_sse2_double.h
-include/gromacs/gmx_sse2_single.h
 include/gromacs/gmx_statistics.h
 include/gromacs/gmx_system_xdr.h
+include/gromacs/gmx_thread_affinity.h
 include/gromacs/gmx_wallcycle.h
+include/gromacs/gmx_x86_avx_128_fma.h
+include/gromacs/gmx_x86_avx_256.h
+include/gromacs/gmx_x86_simd_double.h
+include/gromacs/gmx_x86_simd_single.h
+include/gromacs/gmx_x86_sse2.h
+include/gromacs/gmx_x86_sse4_1.h
 include/gromacs/gmxcomplex.h
 include/gromacs/gmxcpp.h
 include/gromacs/gmxfio.h
 include/gromacs/gpp_atomtype.h
 include/gromacs/gpp_nextnb.h
+include/gromacs/gpu_utils.h
 include/gromacs/grompp.h
 include/gromacs/gstat.h
 include/gromacs/hackblock.h
@@ -164,22 +186,23 @@ include/gromacs/indexutil.h
 include/gromacs/inputrec.h
 include/gromacs/invblock.h
 include/gromacs/macros.h
-include/gromacs/magic.h
 include/gromacs/main.h
 include/gromacs/mainpage.h
 include/gromacs/maths.h
 include/gromacs/matio.h
 include/gromacs/md5.h
+include/gromacs/md_logging.h
+include/gromacs/md_support.h
 include/gromacs/mdatoms.h
 include/gromacs/mdebin.h
 include/gromacs/mdrun.h
-include/gromacs/molfile_plugin.h
 include/gromacs/mpelogging.h
 include/gromacs/mshift.h
 include/gromacs/mtop_util.h
 include/gromacs/mtxio.h
 include/gromacs/mvdata.h
 include/gromacs/names.h
+include/gromacs/nbnxn_cuda_data_mgmt.h
 include/gromacs/nbsearch.h
 include/gromacs/network.h
 include/gromacs/nonbonded.h
@@ -196,16 +219,16 @@ include/gromacs/pdb2top.h
 include/gromacs/pdbio.h
 include/gromacs/perf_est.h
 include/gromacs/physics.h
+include/gromacs/pmalloc_cuda.h
 include/gromacs/pme.h
 include/gromacs/poscalc.h
 include/gromacs/position.h
-include/gromacs/pppm.h
 include/gromacs/princ.h
 include/gromacs/pull.h
+include/gromacs/pull_rotation.h
 include/gromacs/qmmm.h
 include/gromacs/random.h
 include/gromacs/rbin.h
-include/gromacs/rdgroup.h
 include/gromacs/readinp.h
 include/gromacs/resall.h
 include/gromacs/rmpbc.h
@@ -217,6 +240,7 @@ include/gromacs/sfactor.h
 include/gromacs/shellfc.h
 include/gromacs/shift.h
 include/gromacs/sighandler.h
+include/gromacs/sim_util.h
 include/gromacs/smalloc.h
 include/gromacs/sortwater.h
 include/gromacs/sparsematrix.h
@@ -227,6 +251,7 @@ include/gromacs/strdb.h
 include/gromacs/string2.h
 include/gromacs/symtab.h
 include/gromacs/sysstuff.h
+include/gromacs/tables.h
 include/gromacs/tgroup.h
 include/gromacs/thread_mpi.h
 include/gromacs/thread_mpi/atomic.h
@@ -238,16 +263,21 @@ include/gromacs/thread_mpi/atomic/gcc_ppc.h
 include/gromacs/thread_mpi/atomic/gcc_spinlock.h
 include/gromacs/thread_mpi/atomic/gcc_x86.h
 include/gromacs/thread_mpi/atomic/msvc.h
+include/gromacs/thread_mpi/atomic/suncc-sparc.h
 include/gromacs/thread_mpi/atomic/xlc_ppc.h
 include/gromacs/thread_mpi/barrier.h
 include/gromacs/thread_mpi/collective.h
 include/gromacs/thread_mpi/event.h
+include/gromacs/thread_mpi/hwinfo.h
 include/gromacs/thread_mpi/list.h
 include/gromacs/thread_mpi/lock.h
 include/gromacs/thread_mpi/mpi_bindings.h
+include/gromacs/thread_mpi/mutex.h
 include/gromacs/thread_mpi/numa_malloc.h
+include/gromacs/thread_mpi/system_error.h
 include/gromacs/thread_mpi/threads.h
 include/gromacs/thread_mpi/tmpi.h
+include/gromacs/thread_mpi/visibility.h
 include/gromacs/thread_mpi/wait.h
 include/gromacs/tmpi.h
 include/gromacs/topsort.h
@@ -265,19 +295,26 @@ include/gromacs/types/energy.h
 include/gromacs/types/enums.h
 include/gromacs/types/fcdata.h
 include/gromacs/types/filenm.h
+include/gromacs/types/force_flags.h
 include/gromacs/types/forcerec.h
 include/gromacs/types/genborn.h
 include/gromacs/types/globsig.h
 include/gromacs/types/graph.h
 include/gromacs/types/group.h
+include/gromacs/types/hw_info.h
 include/gromacs/types/idef.h
 include/gromacs/types/ifunc.h
 include/gromacs/types/inputrec.h
+include/gromacs/types/interaction_const.h
 include/gromacs/types/ishift.h
 include/gromacs/types/iteratedconstraints.h
 include/gromacs/types/matrix.h
 include/gromacs/types/mdatom.h
+include/gromacs/types/membedt.h
+include/gromacs/types/nb_verlet.h
 include/gromacs/types/nblist.h
+include/gromacs/types/nbnxn_cuda_types_ext.h
+include/gromacs/types/nbnxn_pairlist.h
 include/gromacs/types/nlistheuristics.h
 include/gromacs/types/nrnb.h
 include/gromacs/types/ns.h
@@ -294,10 +331,9 @@ include/gromacs/types/trx.h
 include/gromacs/update.h
 include/gromacs/vcm.h
 include/gromacs/vec.h
+include/gromacs/version.h
 include/gromacs/viewit.h
-include/gromacs/vmddlopen.h
-include/gromacs/vmdio.h
-include/gromacs/vmdplugin.h
+include/gromacs/visibility.h
 include/gromacs/vsite.h
 include/gromacs/warninp.h
 include/gromacs/wgms.h
@@ -306,26 +342,22 @@ include/gromacs/writeps.h
 include/gromacs/xdrf.h
 include/gromacs/xtcio.h
 include/gromacs/xvgr.h
-lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.a
-lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.la
 lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so
 lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
-lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.a
-lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.la
 lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so
 lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
-lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.a
-lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.la
 lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so
 lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
-lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.a
-lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.la
 lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so
 lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
 libdata/pkgconfig/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
+%%DATADIR%%/COPYING
+%%DATADIR%%/CTestTestfile.cmake
+%%DATADIR%%/README.tutor
+%%DATADIR%%/README_FreeEnergyModifications.txt
 %%DATADIR%%/html/gmxfaq.html
 %%DATADIR%%/html/images/1ctf-0.2.jpg
 %%DATADIR%%/html/images/1ctf-0.5.jpg
@@ -354,14 +386,16 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/html/images/flow_vline.gif
 %%DATADIR%%/html/images/flow_vrule.gif
 %%DATADIR%%/html/images/gmxlogo_small.jpg
+%%DATADIR%%/html/images/gmxlogo_small.png
 %%DATADIR%%/html/images/links.gif
 %%DATADIR%%/html/images/mail.gif
 %%DATADIR%%/html/images/manual.gif
 %%DATADIR%%/html/images/plotje.gif
+%%DATADIR%%/html/images/rainbow.gif
 %%DATADIR%%/html/images/software.gif
 %%DATADIR%%/html/images/topologies.gif
 %%DATADIR%%/html/images/xvgr.gif
-%%DATADIR%%/html/online.html
+%%DATADIR%%/html/online/ADD_INCLUDE
 %%DATADIR%%/html/online/cpt.html
 %%DATADIR%%/html/online/dat.html
 %%DATADIR%%/html/online/dlg.html
@@ -377,57 +411,79 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/html/online/flow.html
 %%DATADIR%%/html/online/g87.html
 %%DATADIR%%/html/online/g96.html
+%%DATADIR%%/html/online/g_anadock.html
 %%DATADIR%%/html/online/g_anaeig.html
 %%DATADIR%%/html/online/g_analyze.html
 %%DATADIR%%/html/online/g_angle.html
+%%DATADIR%%/html/online/g_bar.html
 %%DATADIR%%/html/online/g_bond.html
 %%DATADIR%%/html/online/g_bundle.html
 %%DATADIR%%/html/online/g_chi.html
 %%DATADIR%%/html/online/g_cluster.html
+%%DATADIR%%/html/online/g_clustsize.html
 %%DATADIR%%/html/online/g_confrms.html
 %%DATADIR%%/html/online/g_covar.html
+%%DATADIR%%/html/online/g_current.html
 %%DATADIR%%/html/online/g_density.html
 %%DATADIR%%/html/online/g_densmap.html
 %%DATADIR%%/html/online/g_densorder.html
 %%DATADIR%%/html/online/g_dielectric.html
-%%DATADIR%%/html/online/g_dih.html
 %%DATADIR%%/html/online/g_dipoles.html
 %%DATADIR%%/html/online/g_disre.html
 %%DATADIR%%/html/online/g_dist.html
 %%DATADIR%%/html/online/g_dyndom.html
 %%DATADIR%%/html/online/g_enemat.html
 %%DATADIR%%/html/online/g_energy.html
+%%DATADIR%%/html/online/g_filter.html
 %%DATADIR%%/html/online/g_gyrate.html
 %%DATADIR%%/html/online/g_h2order.html
 %%DATADIR%%/html/online/g_hbond.html
 %%DATADIR%%/html/online/g_helix.html
+%%DATADIR%%/html/online/g_helixorient.html
 %%DATADIR%%/html/online/g_lie.html
 %%DATADIR%%/html/online/g_mdmat.html
+%%DATADIR%%/html/online/g_membed.html
 %%DATADIR%%/html/online/g_mindist.html
 %%DATADIR%%/html/online/g_morph.html
 %%DATADIR%%/html/online/g_msd.html
 %%DATADIR%%/html/online/g_nmeig.html
 %%DATADIR%%/html/online/g_nmens.html
+%%DATADIR%%/html/online/g_nmtraj.html
 %%DATADIR%%/html/online/g_order.html
+%%DATADIR%%/html/online/g_polystat.html
 %%DATADIR%%/html/online/g_potential.html
+%%DATADIR%%/html/online/g_principal.html
+%%DATADIR%%/html/online/g_protonate.html
 %%DATADIR%%/html/online/g_rama.html
 %%DATADIR%%/html/online/g_rdf.html
 %%DATADIR%%/html/online/g_rms.html
 %%DATADIR%%/html/online/g_rmsdist.html
 %%DATADIR%%/html/online/g_rmsf.html
 %%DATADIR%%/html/online/g_rotacf.html
+%%DATADIR%%/html/online/g_rotmat.html
 %%DATADIR%%/html/online/g_saltbr.html
 %%DATADIR%%/html/online/g_sas.html
+%%DATADIR%%/html/online/g_select.html
 %%DATADIR%%/html/online/g_sgangle.html
 %%DATADIR%%/html/online/g_sham.html
+%%DATADIR%%/html/online/g_sigeps.html
 %%DATADIR%%/html/online/g_sorient.html
+%%DATADIR%%/html/online/g_spatial.html
+%%DATADIR%%/html/online/g_spol.html
 %%DATADIR%%/html/online/g_tcaf.html
 %%DATADIR%%/html/online/g_traj.html
+%%DATADIR%%/html/online/g_tune_pme.html
+%%DATADIR%%/html/online/g_vanhove.html
 %%DATADIR%%/html/online/g_velacc.html
+%%DATADIR%%/html/online/g_wham.html
+%%DATADIR%%/html/online/g_wheel.html
+%%DATADIR%%/html/online/g_x2top.html
+%%DATADIR%%/html/online/g_xrama.html
 %%DATADIR%%/html/online/genbox.html
 %%DATADIR%%/html/online/genconf.html
 %%DATADIR%%/html/online/genion.html
 %%DATADIR%%/html/online/genpr.html
+%%DATADIR%%/html/online/genrestr.html
 %%DATADIR%%/html/online/getting_started.html
 %%DATADIR%%/html/online/gmxcheck.html
 %%DATADIR%%/html/online/gmxdemo.html
@@ -482,9 +538,11 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/html/online/xtc.html
 %%DATADIR%%/html/online/xvg.html
 %%DATADIR%%/html/online/yourown.html
-%%DATADIR%%/template/Makefile.%%BUILD%%%%SUFFIX_DOUBLE%%
+%%DATADIR%%/html/online.html
+%%DATADIR%%/template/CMakeLists.txt
 %%DATADIR%%/template/Makefile.pkg
 %%DATADIR%%/template/README
+%%DATADIR%%/template/cmake/FindGROMACS.cmake
 %%DATADIR%%/template/template.c
 %%DATADIR%%/top/amber03.ff/aminoacids.arn
 %%DATADIR%%/top/amber03.ff/aminoacids.c.tdb
@@ -711,10 +769,10 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/top/charmm27.ff/aminoacids.vsd
 %%DATADIR%%/top/charmm27.ff/atomtypes.atp
 %%DATADIR%%/top/charmm27.ff/cmap.itp
+%%DATADIR%%/top/charmm27.ff/dna.arn
+%%DATADIR%%/top/charmm27.ff/dna.c.tdb
 %%DATADIR%%/top/charmm27.ff/dna.hdb
 %%DATADIR%%/top/charmm27.ff/dna.n.tdb
-%%DATADIR%%/top/charmm27.ff/dna.c.tdb
-%%DATADIR%%/top/charmm27.ff/dna.arn
 %%DATADIR%%/top/charmm27.ff/dna.rtp
 %%DATADIR%%/top/charmm27.ff/ffbonded.itp
 %%DATADIR%%/top/charmm27.ff/ffnabonded.itp
@@ -726,10 +784,10 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/top/charmm27.ff/ions.itp
 %%DATADIR%%/top/charmm27.ff/lipids.hdb
 %%DATADIR%%/top/charmm27.ff/lipids.rtp
+%%DATADIR%%/top/charmm27.ff/rna.arn
+%%DATADIR%%/top/charmm27.ff/rna.c.tdb
 %%DATADIR%%/top/charmm27.ff/rna.hdb
 %%DATADIR%%/top/charmm27.ff/rna.n.tdb
-%%DATADIR%%/top/charmm27.ff/rna.c.tdb
-%%DATADIR%%/top/charmm27.ff/rna.arn
 %%DATADIR%%/top/charmm27.ff/rna.r2b
 %%DATADIR%%/top/charmm27.ff/rna.rtp
 %%DATADIR%%/top/charmm27.ff/spc.itp
@@ -925,6 +983,7 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/top/highway.dat
 %%DATADIR%%/top/ions.itp
 %%DATADIR%%/top/links.dat
+%%DATADIR%%/top/nsfactor.dat
 %%DATADIR%%/top/oplsaa.ff/1propanol.itp
 %%DATADIR%%/top/oplsaa.ff/aminoacids.c.tdb
 %%DATADIR%%/top/oplsaa.ff/aminoacids.hdb
@@ -952,6 +1011,8 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/top/ps.m2p
 %%DATADIR%%/top/random.dat
 %%DATADIR%%/top/refi_aa.dat
+%%DATADIR%%/top/residues.dtd
+%%DATADIR%%/top/residues.xml
 %%DATADIR%%/top/residuetypes.dat
 %%DATADIR%%/top/sfactor.dat
 %%DATADIR%%/top/spc.itp
@@ -970,47 +1031,9 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/top/tip4p.gro
 %%DATADIR%%/top/tip4p.itp
 %%DATADIR%%/top/tip5p.gro
+%%DATADIR%%/top/vdw-msms.dat
 %%DATADIR%%/top/vdwradii.dat
 %%DATADIR%%/top/xlateat.dat
-%%DATADIR%%/tutor/gmxdemo/cpeptide.pdb
-%%DATADIR%%/tutor/gmxdemo/demo
-%%DATADIR%%/tutor/methanol/conf.gro
-%%DATADIR%%/tutor/methanol/grompp.mdp
-%%DATADIR%%/tutor/methanol/index.ndx
-%%DATADIR%%/tutor/methanol/methanol.itp
-%%DATADIR%%/tutor/methanol/methanol.pdb
-%%DATADIR%%/tutor/methanol/topol.top
-%%DATADIR%%/tutor/mixed/conf.gro
-%%DATADIR%%/tutor/mixed/grompp.mdp
-%%DATADIR%%/tutor/mixed/index.ndx
-%%DATADIR%%/tutor/mixed/mixed.pdb
-%%DATADIR%%/tutor/mixed/topol.top
-%%DATADIR%%/tutor/nmr1/conf.gro
-%%DATADIR%%/tutor/nmr1/grompp.mdp
-%%DATADIR%%/tutor/nmr1/pep.pdb
-%%DATADIR%%/tutor/nmr1/topol.top
-%%DATADIR%%/tutor/nmr2/conf.gro
-%%DATADIR%%/tutor/nmr2/genconf.gcp
-%%DATADIR%%/tutor/nmr2/grompp.mdp
-%%DATADIR%%/tutor/nmr2/pep.pdb
-%%DATADIR%%/tutor/nmr2/topol.top
-%%DATADIR%%/tutor/speptide/em.mdp
-%%DATADIR%%/tutor/speptide/full.mdp
-%%DATADIR%%/tutor/speptide/pr.mdp
-%%DATADIR%%/tutor/speptide/speptide.pdb
-%%DATADIR%%/tutor/water/conf.gro
-%%DATADIR%%/tutor/water/grompp.mdp
-%%DATADIR%%/tutor/water/index.ndx
-%%DATADIR%%/tutor/water/spc216.pdb
-%%DATADIR%%/tutor/water/topol.top
-@dirrm %%DATADIR%%/tutor/water
-@dirrm %%DATADIR%%/tutor/speptide
-@dirrm %%DATADIR%%/tutor/nmr2
-@dirrm %%DATADIR%%/tutor/nmr1
-@dirrm %%DATADIR%%/tutor/mixed
-@dirrm %%DATADIR%%/tutor/methanol
-@dirrm %%DATADIR%%/tutor/gmxdemo
-@dirrm %%DATADIR%%/tutor
 @dirrm %%DATADIR%%/top/oplsaa.ff
 @dirrm %%DATADIR%%/top/gromos53a6.ff
 @dirrm %%DATADIR%%/top/gromos53a5.ff
@@ -1030,6 +1053,7 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 @dirrm %%DATADIR%%/top/amber94.ff
 @dirrm %%DATADIR%%/top/amber03.ff
 @dirrm %%DATADIR%%/top
+@dirrm %%DATADIR%%/template/cmake
 @dirrm %%DATADIR%%/template
 @dirrm %%DATADIR%%/html/online
 @dirrm %%DATADIR%%/html/images