Removed old

Package-Manager: portage-2.1.9.42/cvs/Linux i686

5 files changed, 13 insertions, 832 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 6629662e4621..938e46814f6b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.78 2011/04/04 18:46:56 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.79 2011/04/04 18:56:42 ottxor Exp $
+
+  04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.7-r5.ebuild,
+  -gromacs-4.5.3.ebuild, -gromacs-4.5.3-r3.ebuild:
+  Removed old
 
   04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4.ebuild:
   Removed sse use flag (fixed bug #361933)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index d7aa8ac62ca5..ce686ff5e8cb 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -5,9 +5,7 @@ AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e3
 DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
 DIST gromacs-4.0.7.tar.gz 8404518 RMD160 4fa8e5c90f549ef627a98a907a166676692a4c4b SHA1 8519bef2fa989fb487d54612b0a2d0228f228b30 SHA256 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
-DIST gromacs-4.0.7_missing_distfiles.patch.bz2 5696 RMD160 b49b6e99e00cfcc1cda3a7f28c3a508d7e2c482d SHA1 8812d13e746d35d2b2b2d1e2224ffd6b60973bc2 SHA256 a648c9da000f44749eb6964c668523059125aab29946a08a6b2d22a90637363c
 DIST gromacs-4.0.7_upstream2010-06-08.patch.gz 11876 RMD160 d65c9cf0386319953113ac1a5dc548768a745345 SHA1 823a72c4126d789ae38921bd46743414d4f391c1 SHA256 91d3eee79a0ec20df506e59bab789fe15428b4323548af5f97ccbae506036879
-DIST gromacs-4.0.7_upstream2010-09-15.patch.bz2 21551 RMD160 a3d40f6932ea7c10a1d1f3cbce21269b58b0949b SHA1 809c823717f36e334a132ed844dbfccba84b13f9 SHA256 3c9d2ad09f855c67e8b4d042a1ee77bad88e78fb0de047eb314e8e4c4e58600f
 DIST gromacs-4.5.3.tar.gz 10338471 RMD160 2bb9cab3c611b93c4323e16b0d171c16cd407bf1 SHA1 c4845e5e62d1f53ee443301dad00138feba6d275 SHA256 d298b81b172c2ab36b8fab8f1d3091dc48e283f35a1574bf7f9f0df382074e06
 DIST gromacs-4.5.3_upstream20110217.patch.bz2 595080 RMD160 fb5b5f656018b64980517d9ad1083cb83d45288c SHA1 b1fd6c05ce9333ee86392d1725f64556aa4d4012 SHA256 c3234e0eb331d688e7416302a93c3da4b451fe32459e369e9341bbfd927c9743
 DIST gromacs-4.5.4.tar.gz 10353984 RMD160 96065d1a173231f75869764a08eb4feccc1ec597 SHA1 c7b3fbd2f3ddf915bc082e7effe76a8276563726 SHA256 301cc3d790f5036e230e02b1fb03c9b92e0db13df7ac6dbffb2a2fb03d7a1d1c
@@ -15,21 +13,18 @@ DIST gromacs-manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de50
 DIST gromacs-manual-4.5.3.pdf 2438528 RMD160 07f5ec0db1a773e77806c79554e5bb4fa8533dfd SHA1 7c81fc18e426d1090c485968d81957977ff10fc9 SHA256 6794fca3a2125918a03cd6bae3c031ab9b213c42a5f68a720c955b9107508717
 DIST gromacs-manual-4.5.4.pdf 2463242 RMD160 309a1d9bc5f4821076d53f668c36f1c6bfc1714f SHA1 58c0261308212af29fa0c4f4a6d1b81da6d84766 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252
 EBUILD gromacs-4.0.7-r4.ebuild 9967 RMD160 168b3d2e5273634e710d45e293845ef6e97dd518 SHA1 4fb7f526ed22f2069e955317d8076f0446c3ca53 SHA256 b827418a2513499f9faaddac78450e1fc3245a9b392fd30692db179a1e130748
-EBUILD gromacs-4.0.7-r5.ebuild 9632 RMD160 9793eff619750d001a619bc90eccc977e6c0d12a SHA1 c98731aa5a9b5265839be712e35b1b73864b5ce7 SHA256 4b275be64d364867e4fb25dfc66c5405647f32b66cb2d7c453e0e471ee5d3eb9
-EBUILD gromacs-4.5.3-r3.ebuild 8076 RMD160 d25cab9b9d4c8c1044f7a8f7ea2d60013ee634a8 SHA1 9a57f25a332769c0beae388513e2211c93f65409 SHA256 23b5e142335b35def423d334fcac2ed9def829b47fd3b242a8352bc545bb2bf2
 EBUILD gromacs-4.5.3-r4.ebuild 8119 RMD160 416df204a948bd7ed224d16827565f6da1446b67 SHA1 18c3836131f570e6378abb61607f5ceb293abb5c SHA256 7b1ba5a26a7f8d7636dfc240c21c4238c0534f78551ebd0b04b376253a7ff46d
-EBUILD gromacs-4.5.3.ebuild 7804 RMD160 79ac411bf838927697c419eaaf9d36ed698662e1 SHA1 176a781a35c1a568b106261723cf724a123824f2 SHA256 99174a1320e0b3334722aa1a3dcef7df92ae7a86912cbf027ebab1d8f10e177a
 EBUILD gromacs-4.5.4.ebuild 7988 RMD160 3b6fa3eaf3a3bb93b52c7f6be7590f62c6d1b697 SHA1 2d65cb9fe402d68da1d4e9a4fdeff47a09d8c26c SHA256 350a167152abdbd250a1afe6d14d2e4c0bb58c25c8839c6e8ff9885dbf1d2015
-MISC ChangeLog 14434 RMD160 3770dfdd25c220afab0ec89139f353e58a870c2c SHA1 e3e866929a343ba5067d82a8918962ad7abcc0c4 SHA256 7fa8460497257e10ffebc9529f8866a084136cac5c3ead9e0afaa7133adf6625
+MISC ChangeLog 14580 RMD160 f70826d61301861f7b2559f5252efed0e09a0495 SHA1 79a8f45668151b535eeab07ee0836948ec57dcf7 SHA256 c2f73c9754e0d15e1e93640f30a27f05d4ca023b14d5a9aa8591623690ce0d96
 MISC metadata.xml 576 RMD160 376a5b9f0b65c82cfe2cb0f3d7fe81b593932fa2 SHA1 5c4da5764221ae19041b8a3665ea2205c71598c6 SHA256 a08022560f16532545db516b50a9f84c112b34e5ae406a778bdaef5046e226fd
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diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild
deleted file mode 100644
index 0744795ddb66..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild
+++ /dev/null
@@ -1,300 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r5.ebuild,v 1.3 2011/03/02 17:55:01 jlec Exp $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-inherit autotools bash-completion eutils multilib toolchain-funcs
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		mirror://gentoo/${P}_upstream2010-09-15.patch.bz2
-		mirror://gentoo/${P}_missing_distfiles.patch.bz2
-		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf -> gromacs-manual-4.0.pdf )
-		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
-mpi +single-precision static static-libs test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
-use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
-
-src_prepare() {
-
-	( use single-precision || use double-precision ) || \
-		die "Nothing to compile, enable single-precision and/or double-precision"
-
-	if use static; then
-		use X && die "You cannot compile a static version with X support, disable X or static"
-		use xml && die "You cannot compile a static version with xml support
-		(see bug #306479), disable xml or static"
-	fi
-
-	epatch "${WORKDIR}/${P}_upstream2010-09-15.patch"
-	epatch "${WORKDIR}/${P}_missing_distfiles.patch"
-	sed -e '/AC_INIT/s/4\.0\.7/&-2010-09-15/' -i configure.ac \
-		|| die "Failed to change version in configure.ac"
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	epatch_user
-	eautoreconf
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" single"
-	use double-precision && GMX_DIRS+=" double"
-	for x in ${GMX_DIRS}; do
-		mkdir "${S}-${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
-		use mpi || continue
-		mkdir "${S}-${x}_mpi" || die
-	done
-}
-
-src_configure() {
-	local myconf
-	local myconfsingle
-	local myconfdouble
-	local suffixdouble
-
-	#leave all assembly options enabled mdrun is smart enough to deside itself
-	#there so no gentoo on bluegene!
-	myconf="${myconf} --disable-bluegene"
-
-	#from gromacs configure
-	if ! use fftw; then
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 4.1 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-		myconf="${myconf} --enable-fortran"
-	else
-		myconf="${myconf} --disable-fortran"
-	fi
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${LIBS} -lblas"
-		myconf="${myconf} $(use_with blas external-blas)"
-	fi
-
-	# if we need external lapack
-	if use lapack; then
-		export LIBS="${LIBS} -llapack"
-		myconf="${myconf} $(use_with lapack external-lapack)"
-	fi
-
-	# by default its better to have dynamicaly linked binaries
-	if use static; then
-		#gmx build static libs by default
-		myconf="${myconf} --disable-shared $(use_enable static all-static)"
-	else
-		myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
-	fi
-
-	myconf="--datadir="${EPREFIX}"/usr/share \
-			--bindir="${EPREFIX}"/usr/bin \
-			--libdir="${EPREFIX}"/usr/$(get_libdir) \
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
-			$(use_with dmalloc) \
-			$(use_with fftw fft fftw3) \
-			$(use_with gsl) \
-			$(use_with X x) \
-			$(use_with xml) \
-			${myconf}"
-
-	#if we build single and double - double is suffixed
-	if ( use double-precision && use single-precision ); then
-		suffixdouble="_d"
-	else
-		suffixdouble=""
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
-	myconfsingle="${myconf} --enable-float --program-suffix=''"
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		cd "${S}-${x}"
-		local p=myconf${x}
-		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		einfo "Compiling for ${x} precision"
-		emake || die "emake for ${x} precision failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake mdrun || die "emake mdrun for ${x} precision failed"
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${S}-${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
-	done
-	#we have pkg-config files
-	rm "${ED}"/usr/$(get_libdir)/*.la
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	dobashcompletion "${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.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL README
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-4.0.pdf" "manual-4.0.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-
-	if use ffamber; then
-		use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
-		# prepare vdwradii.dat
-		cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
-			SOL  MW    0
-			SOL  LP    0
-		EOF
-		# regenerate aminoacids.dat
-		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
-		| awk '{print $1}' | sort -u | tail -n+4 | wc -l \
-		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
-		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
-		| awk '{print $1}' | sort -u | tail -n+4 \
-		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
-		mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat
-		# copy ff files
-		for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
-				ffamberGS ffamberGSs ffamber03 ; do
-			einfo "Adding ${x} to gromacs"
-			cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
-		done
-		# copy suplementary files
-		cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
-		cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
-		# actualy add records to FF.dat
-		cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
-			ffamber94   AMBER94 Cornell protein/nucleic forcefield
-			ffamber96   AMBER96 Kollman protein/nucleic forcefield
-			ffamberGS   AMBER-GS Garcia &  Sanbonmatsu forcefield
-			ffamberGSs  AMBER-GSs Nymeyer &  Garcia forcefield
-			ffamber99   AMBER99 Wang protein/nucleic acid forcefield
-			ffamber99p  AMBER99p protein/nucleic forcefield
-			ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
-			ffamber03   AMBER03 Duan protein/nucleic forcefield
-		EOF
-		cat "${ED}"/usr/share/gromacs/top/FF.dat \
-			"${ED}"/usr/share/gromacs/top/FF.dat.new \
-			| tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
-		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
-			"${ED}"/usr/share/gromacs/top/FF.dat
-		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
-			"${ED}"/usr/share/gromacs/top/FF.dat
-		rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
-	fi
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
deleted file mode 100644
index cdf58f62e996..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
+++ /dev/null
@@ -1,260 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild,v 1.2 2011/03/02 17:55:01 jlec Exp $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
-
-inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? (
-		http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git
-else
-	PATCHES=( ${WORKDIR}/${P}_upstream20110217.patch )
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-	mirror://gentoo/${P}_upstream20110217.patch.bz2"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-#gromacs has gnu exec stacks for speedup
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
-src_prepare() {
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	autotools-utils_src_prepare || die
-
-	sed -e '/AC_INIT/s/4\.5\.3-dev/4.5.3-2011-02-17/' -i configure.ac \
-		|| die "Failed to change version in configure.ac"
-
-	eautoreconf || die
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	#from gromacs configure
-	if ! use fftw; then
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 5.0 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		use threads && eerror "You cannot compile fortran kernel with threads"
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	# if we need external blas or lapack
-	use blas && export LIBS+=" -lblas"
-	use lapack && export LIBS+=" -llapack"
-	local sseflag="x86-64-sse"
-	use x86 && sseflag="ia32-sse"
-
-	#a bug in gromacs autotools
-	use sse && append-flags -msse
-	use sse2 && append-flags -msse2
-
-	for x in ${GMX_DIRS}; do
-		local suffix="" sse="sse"
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		#double uses sse2, single sse
-		[ "${x}" = "double" ] && sse="sse2"
-		myeconfargs=(
-			--bindir="${EPREFIX}"/usr/bin
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
-			--enable-"${x}"
-			$(use_with dmalloc)
-			$(use_with fftw fft fftw3)
-			$(use_with gsl)
-			$(use_with X x)
-			$(use_with xml)
-			$(use_enable threads)
-			$(use_enable altivec ppc-altivec)
-			$(use_enable ia64 ia64-asm)
-			$(use_with lapack external-lapack)
-			$(use_with blas external-blas)
-			$(use_enable fkernels fortran)
-			--disable-bluegene
-			--disable-la-files
-			--disable-power6
-			--disable-ia32-sse
-			--disable-x86-64-sse
-			$(use_enable $sse $sseflag)
-		)
-		#disable ia32-sse and x86-64-sse and enable what we really need in last line
-
-		einfo "Configuring for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			autotools-utils_src_install
-		use mpi || continue
-		#autotools-utils_src_install does not support args
-		#using autotools-utils_src_compile instead
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
-
-		#stolen from autotools-utils_src_install see comment above
-		local args
-		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
-		remove_libtool_files ${args}
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	dobashcompletion "${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.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(g_luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.3.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3.ebuild
deleted file mode 100644
index bf3313ee566d..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.3.ebuild
+++ /dev/null
@@ -1,258 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.3.ebuild,v 1.3 2011/03/02 17:55:01 jlec Exp $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
-
-inherit autotools bash-completion eutils multilib toolchain-funcs
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision static static-libs test +threads +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
-use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
-
-src_prepare() {
-
-	( use single-precision || use double-precision ) || \
-		die "Nothing to compile, enable single-precision and/or double-precision"
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	if use static; then
-		use X && die "You cannot compile a static version with X support, disable X or static"
-		use xml && die "You cannot compile a static version with xml support
-		(see bug #306479), disable xml or static"
-	fi
-	epatch_user
-	eautoreconf
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" single"
-	use double-precision && GMX_DIRS+=" double"
-	for x in ${GMX_DIRS}; do
-		mkdir "${S}-${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
-		use mpi || continue
-		mkdir "${S}-${x}_mpi" || die
-	done
-}
-
-src_configure() {
-	local myconf
-	local myconfsingle
-	local myconfdouble
-	local suffixdouble
-
-	#leave all assembly options enabled mdrun is smart enough to deside itself
-	#there so no gentoo on bluegene!
-	myconf="${myconf} --disable-bluegene"
-
-	#we have pkg-config files
-	myconf="${myconf} --disable-la-files"
-
-	#from gromacs configure
-	if ! use fftw; then
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 4.1 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		use threads && die "You cannot compile fortran kernel with threads"
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-		myconf="${myconf} --enable-fortran"
-	else
-		myconf="${myconf} --disable-fortran"
-	fi
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${LIBS} -lblas"
-		myconf="${myconf} $(use_with blas external-blas)"
-	fi
-
-	# if we need external lapack
-	if use lapack; then
-		export LIBS="${LIBS} -llapack"
-		myconf="${myconf} $(use_with lapack external-lapack)"
-	fi
-
-	# by default its better to have dynamicaly linked binaries
-	if use static; then
-		#gmx build static libs by default
-		myconf="${myconf} --disable-shared $(use_enable static all-static)"
-	else
-		myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
-	fi
-
-	myconf="--datadir="${EPREFIX}"/usr/share \
-			--bindir="${EPREFIX}"/usr/bin \
-			--libdir="${EPREFIX}"/usr/$(get_libdir) \
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
-			$(use_with dmalloc) \
-			$(use_with fftw fft fftw3) \
-			$(use_with gsl) \
-			$(use_with X x) \
-			$(use_with xml) \
-			$(use_enable threads) \
-			${myconf}"
-
-	#if we build single and double - double is suffixed
-	if ( use double-precision && use single-precision ); then
-		suffixdouble="_d"
-	else
-		suffixdouble=""
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
-	myconfsingle="${myconf} --enable-float --program-suffix=''"
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		cd "${S}-${x}"
-		local p=myconf${x}
-		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		einfo "Compiling for ${x} precision"
-		emake || die "emake for ${x} precision failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake mdrun || die "emake mdrun for ${x} precision failed"
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${S}-${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	dobashcompletion "${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.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(g_luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	elog
-}