sci-chemistry/gromacs: moved to gx86

9 files changed, 0 insertions, 1687 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
deleted file mode 100644
index 1fed511a1..000000000
--- a/sci-chemistry/gromacs/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gromacs-2016-rc1.tar.gz 27322876 SHA256 69a307009cd9015b09af3c39ed4b193e71c59deccc3b34e758b3b9b5a34f7a47 SHA512 9c74ab718c9c894525524c0612aac93246be8aff86491f4b4854783d5e112c346b8c6bd185ec951a76aa398fdb2132abf42bb27b644440ceb6f6baeeede9c3a0 WHIRLPOOL cdb4d417770720069c6e1de2930d36f3a952ce9b2d111d1dd9a2f3b87d28cc199a17745db2c580da6606eb9dd59dfd9c4ddb5297de08202067dee0160a3a985e
-DIST regressiontests-2016-rc1.tar.gz 66629314 SHA256 63fcf8fcb1371478b705dd8f44f2c284ac8c6f3e7eb8146f751f6e0e0f2db415 SHA512 8900efb605d69aa723bab398556a9b0d94da2b25d55948a3903f2d5a47c0f89306fffe3b0c7e780508b301463243bc73191a9dee6494ab288ca89831e71f741a WHIRLPOOL a205113884c65de4e9a75f0af59a1be910cf82a7fca8ba561c13815793f98ee0af342a0318044c49c757c8b25cfebb8b42299e885345e7f1af695f2e2b591297
diff --git a/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch b/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch
deleted file mode 100644
index f39921f69..000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff -Naur gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake
---- gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake	1969-12-31 17:00:00.000000000 -0700
-+++ gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake	2013-05-03 10:47:52.779868731 -0600
-@@ -0,0 +1,13 @@
-+
-+# This a modified version of CMakeASMInformation.cmake coming with cmake 2.8.6, which
-+# supports .S files
-+
-+# support for AT&T syntax assemblers, e.g. GNU as
-+
-+SET(ASM_DIALECT "-ATT")
-+SET(CMAKE_ASM${ASM_DIALECT}_SOURCE_FILE_EXTENSIONS S;s;asm)
-+
-+SET(CMAKE_ASM${ASM_DIALECT}_COMPILE_OBJECT "<CMAKE_ASM${ASM_DIALECT}_COMPILER> <FLAGS> -o <OBJECT> <SOURCE>")
-+
-+INCLUDE(CMakeASMInformation)
-+SET(ASM_DIALECT)
-diff -Naur gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt gromacs-4.5.7/src/gmxlib/CMakeLists.txt
---- gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt	2013-05-03 10:46:29.029305075 -0600
-+++ gromacs-4.5.7/src/gmxlib/CMakeLists.txt	2013-05-03 10:50:34.630582295 -0600
-@@ -47,18 +47,18 @@
- if(GMX_IA32_ASM)
-   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_ia32_${SSETYPE}/*.c)
-   if(GMX_ASM_USEASM_NASM)
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.s)    
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.S)    
-   else()
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.S)
-   endif()
- endif(GMX_IA32_ASM)
- 
- if(GMX_X86_64_ASM)
-   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_x86_64_${SSETYPE}/*.c)
-   if(GMX_ASM_USEASM_NASM)
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.S)
-   else()
--    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.s)
-+    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.S)
-   endif()
- endif(GMX_X86_64_ASM)
- 
diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
deleted file mode 100644
index 1ca034301..000000000
--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
+++ /dev/null
@@ -1,266 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
deleted file mode 100644
index 1ca034301..000000000
--- a/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
+++ /dev/null
@@ -1,266 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
deleted file mode 100644
index e00c4f963..000000000
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ /dev/null
@@ -1,263 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-TEST_PV="4.6.6"
-MANUAL_PV="4.6.6"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-6"
-	inherit git-r3
-	LIVE_DEPEND="doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
-	LIVE_DEPEND=""
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	${LIVE_DEPEND}
-	doc? ( app-doc/doxygen )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use doc; then
-			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/manual"\
-				git-r3_src_unpack
-		fi
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_GSL=$(usex gsl)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" -DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		#manual can only be build after gromacs was installed once in image
-		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
-			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
-			BUILD_DIR="${WORKDIR}"/manual_build \
-				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
-			[[ ${CHOST} = *-darwin* ]] && \
-				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
-			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
-			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
-			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			DESTDIR="${D}" cmake-utils_src_make install-mdrun
-	done
-
-	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"usr/bin/completion.*
-	rm -rf "${ED}"usr/share/gromacs/html
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
deleted file mode 100644
index 5d1717e09..000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ /dev/null
@@ -1,284 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_COMMIT="master" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_SYMLINK_OLD_BINARY_NAMES=$(usex make-symlinks)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion, not 100% necessary for
-		# rel ebuilds as bundled
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		#release ebuild does this automatically
-		if [[ $PV = *9999* ]]; then
-			cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die
-			echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
-	#little hacckery as some gmx-completion* newlines ,so cat won't work
-	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
-		echo $(<${x})
-	done > "${T}"/gmx-bashcomp || die
-	newbashcomp "${T}"/gmx-bashcomp gmx
-	bashcomp_alias gmx mdrun
-	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
-	if use double-precision && use single-precision; then
-		bashcomp_alias gmx gmx_d
-		bashcomp_alias gmx mdrun_d
-	fi
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
deleted file mode 100644
index 9711c228e..000000000
--- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
+++ /dev/null
@@ -1,269 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
deleted file mode 100644
index 1ca034301..000000000
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ /dev/null
@@ -1,266 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
deleted file mode 100644
index e98cd51fc..000000000
--- a/sci-chemistry/gromacs/metadata.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>ottxor@gentoo.org</email>
-    <name>Christoph Junghans</name>
-  </maintainer>
-  <maintainer type="person">
-	  <email>alexxy@gentoo.org</email>
-	  <name>Alexey Shvetsov</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <use>
-    <flag name="cuda">Enable cuda non-bonded kernels</flag>
-    <flag name="double-precision">More precise calculations at the expense of speed</flag>
-    <flag name="single-precision">Single precision version of gromacs (default)</flag>
-	<flag name="boost">Enable external boost library</flag>
-	<flag name="hwloc">Enable HWLoc lib support</flag>
-    <flag name="tng">Enable new trajectory format - tng</flag>
-    <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
-    <!-- acceleration optimization flags -->
-    <flag name="offensive">Enable gromacs partly offensive quotes</flag>
-    <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
-  </use>
-</pkgmetadata>