sci/sci-chemistry/gromacs: sync with tree and removed old versions

(Portage version: 2.1.6.13/git/Linux i686)
 (Signed Manifest commit)

12 files changed, 216 insertions, 1075 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0f35b2801..d204553a1 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,7 +1,15 @@
 # ChangeLog for sci-chemistry/gromacs
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-3.3.9999.ebuild, -gromacs-4.0.4.ebuild,
+  -files/gromacs-4.0.4-sparc-cyclecounter.patch, -gromacs-4.0.5-r1.ebuild,
+  -files/gromacs-4.0.5-docdir.patch,
+  -files/gromacs-4.0.5-path-overflow.patch, gromacs-4.0.9999.ebuild,
+  +files/gromacs-4.0.9999-docdir.patch, gromacs-9999.ebuild:
+  sync with tree and removed old ebuilds
+
   30 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
   files/gromacs-4.0.5-docdir.patch:
   docdir -> htmldir
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index e3b1fef75..a06dcef16 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -2,24 +2,17 @@
 Hash: SHA1
 
 AUX gromacs-4.0.4-configure-gfortran.patch 731 RMD160 1ccea4fafd6837461114fc36bc31db4f9390fc08 SHA1 0ec79e9ab691cbae5f116adaa3245ef0b123a598 SHA256 5b902eac127bc84e188224fbfe0182ab3fa3b03c200325ada9cd628bb913b479
-AUX gromacs-4.0.4-sparc-cyclecounter.patch 492 RMD160 0edd643a6dc11820e9785561f03047795044311f SHA1 66c0339c308b3d661def0e184311be510e804c3b SHA256 01565b45b73b32d8d6f83bf1fdf750de4215b24935d992c81191a52d01eb6bed
-AUX gromacs-4.0.5-docdir.patch 2907 RMD160 271f4ccc401cfa03ca3b2b911d0c15ec1fc55d3a SHA1 f6361e2b07cae020a6548c50dacb24611d701d43 SHA256 258a76992ed840ad242a1bf1799a2d83dbf860af85e74b154446acf252a2714a
-AUX gromacs-4.0.5-path-overflow.patch 3577 RMD160 3672abfd43760f02a111df492096f1c35443f07f SHA1 a0c9b74f9216fce870bc8559b71f2a68de26e128 SHA256 9a20e199ca3132c526f7e57939ee098ac7e508ae27e73d7cb3fad2514acdb383
+AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
-DIST gromacs-4.0.4.tar.gz 8443779 RMD160 f90327814170c26a43d99fe7587357a46989fdec SHA1 9466f3ab95d60c0aba8916b1fcc70129cb4e4d72 SHA256 8aefd03cd3269e85c84427f05ceea6d3e16874cd4a90bf3f6fec2b2be24c426f
-DIST gromacs-4.0.5.tar.gz 8465397 RMD160 4c2344629307f3a3daa11b986153d65883a44783 SHA1 9969aae6f77e2216add22a7b29805c4de8df649f SHA256 436b7a2a1ba3637eb07e30d676d78962008373a28fd17a3d889fa5816ca30339
 DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
-EBUILD gromacs-3.3.9999.ebuild 6640 RMD160 e0a39da394ae160584d394bcac9cae89d001d229 SHA1 4be6d054002faf7c4a853f1ee7aad09b2da86b1d SHA256 be6ff76414e9569fc0b160e2e591d749c2e46ae975535ec34332e2d6072b2a46
-EBUILD gromacs-4.0.4.ebuild 6899 RMD160 ea01958dddb6e8874410e01df9171c5e081d1856 SHA1 7e1f7e37a88ecea0840e58d3687d6b00d70b0e0f SHA256 ff452e5d24885bc5ec40fc3ca29fe1f5f6997c499667bf62ebfb6b6a23532a07
-EBUILD gromacs-4.0.5-r1.ebuild 6777 RMD160 cd129e99f4b87c6593b3c1d857eaa2fce97f592e SHA1 2abe23fc342a47bc40945cf0e3c6416d80dbfa09 SHA256 de2f9b23829e5db5d3536cd3b3a5f6b6f117ecd495ef55a781dd930d1c974d73
-EBUILD gromacs-4.0.9999.ebuild 6640 RMD160 c48a23acd60c4943b466cbfe36cc1a10ca5d2327 SHA1 137f0801ffb4fe3a87e3881fa95d432eb3e1041b SHA256 a1a81ae8997d31d956b7aaacc00b8988d6d95c8267c82a5110656856d982441b
-EBUILD gromacs-9999.ebuild 6606 RMD160 c25d3da0f931cee5cd29b7b698025b024b8c33f5 SHA1 3ede827e2fcc2b73ce709af9ff9e5af496c754d8 SHA256 07b3051e743d20b94c2f0df4360d00abad900a1baaad9a76c2924c0a373878fa
-MISC ChangeLog 1931 RMD160 492cc56cc43a8deb1de1036857ba00ddad87ac9f SHA1 8d84809aa9102946d43f6b13ceea01ade55583ea SHA256 e78a224d4cb33429151fb75a4ac9b40b2222aa7a2a7ac5a6b5654635610f53fd
-MISC metadata.xml 642 RMD160 885e11bdae2d4e79b5fd7b48113f44d987c62b19 SHA1 ab77d33e2f7a8e8d6aa8a997e9247fd61bd17a74 SHA256 6e3242563fd78de425260bf28a07a017afb294898a80e02bacef59ec4a83064c
+EBUILD gromacs-4.0.9999.ebuild 6912 RMD160 3a81db2ce3d8b5684251d4671adeafb53d99f53b SHA1 5e05cb08923c2332c5fb48962331d5a43b53dbc9 SHA256 edda284fdfda3188c4b026bb8554d8572977953443078d76656d2ccda7ab780a
+EBUILD gromacs-9999.ebuild 6909 RMD160 5e59f6c97768e288c3861fd8a640e61695c30e03 SHA1 05b6fc388ca0346c640a30545d6745c865988bc5 SHA256 d05a8444d78bf36df7ff83ed28a130dc3664a206e4d4607dcdf877e54eb1ff4e
+MISC ChangeLog 2322 RMD160 b9d4dba80b67f6d59f0bde699838001130a19326 SHA1 262bf96fd45256b4aacf69cf012101f57c777ef7 SHA256 57daa56892090fa3421d12aa17d4ff25663b05efe02109023e816996114f4105
+MISC metadata.xml 580 RMD160 06a95696ec536dd91eab06946d8787546f1e0582 SHA1 b6c5f5e50b518efa3014b69f97307d62734a288d SHA256 e976e31a9e16e9eea09d5ec147ce91d16b4e463453e71ebfb8092485589a6b49
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.11 (GNU/Linux)
 
-iEYEARECAAYFAksULMkACgkQy0OE/ans1/kXEgCeNhtzeERv+hmWzA5RZ8EGgcK3
-chMAn18cgcYn7GolZgHX+7UwKTpnZdSj
-=PWG4
+iEYEARECAAYFAktX/ygACgkQy0OE/ans1/mUtgCeJuPwSiZPGgqINFJIaEfORtuD
+qWYAn1J64RjGxWRC5jCXJOyc8VWuSIys
+=K+3g
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diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.4-sparc-cyclecounter.patch b/sci-chemistry/gromacs/files/gromacs-4.0.4-sparc-cyclecounter.patch
deleted file mode 100644
index f174aef27..000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.4-sparc-cyclecounter.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur gromacs-4.0.4-orig/include/gmx_cyclecounter.h gromacs-4.0.4/include/gmx_cyclecounter.h
---- gromacs-4.0.4-orig/include/gmx_cyclecounter.h	2009-05-09 18:46:02.000000000 +0200
-+++ gromacs-4.0.4/include/gmx_cyclecounter.h	2009-05-09 18:56:50.000000000 +0200
-@@ -408,7 +408,7 @@
- static __inline__ gmx_cycles_t gmx_cycles_read(void)
- { 
-     /* gcc inline assembly on sparc v9 */
--    ticks ret;
-+    unsigned long ret;
-     __asm__("rd %%tick, %0" : "=r" (ret));
-     return ret;  
- }
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.5-docdir.patch b/sci-chemistry/gromacs/files/gromacs-4.0.5-docdir.patch
deleted file mode 100644
index b556947b9..000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.5-docdir.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff -Naur gromacs-4.0.5.orig/share/html/Makefile.am gromacs-4.0.5/share/html/Makefile.am
---- gromacs-4.0.5.orig/share/html/Makefile.am	2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/Makefile.am	2009-11-29 22:27:24.000000000 +0100
-@@ -4,7 +4,7 @@
- #
- SUBDIRS = .  images  online
- 
--htmldir = ${pkgdatadir}/html
-+htmldir = @htmldir@/html
- 
- html_DATA = online.html gmxfaq.html
- 
-diff -Naur gromacs-4.0.5.orig/share/html/Makefile.in gromacs-4.0.5/share/html/Makefile.in
---- gromacs-4.0.5.orig/share/html/Makefile.in	2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/Makefile.in	2009-11-29 22:28:16.000000000 +0100
-@@ -172,7 +172,7 @@
- host_cpu = @host_cpu@
- host_os = @host_os@
- host_vendor = @host_vendor@
--htmldir = ${pkgdatadir}/html
-+htmldir = @htmldir@/html
- includedir = @includedir@
- infodir = @infodir@
- install_sh = @install_sh@
-diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.am gromacs-4.0.5/share/html/images/Makefile.am
---- gromacs-4.0.5.orig/share/html/images/Makefile.am	2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/images/Makefile.am	2009-11-29 23:00:57.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--imagedir = ${pkgdatadir}/html/images
-+imagedir = @htmldir@/html/images
- 
- image_DATA = \
- 	features.gif					\
-diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.in gromacs-4.0.5/share/html/images/Makefile.in
---- gromacs-4.0.5.orig/share/html/images/Makefile.in	2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/images/Makefile.in	2009-11-29 23:01:20.000000000 +0100
-@@ -186,7 +186,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--imagedir = ${pkgdatadir}/html/images
-+imagedir = @htmldir@/html/images
- image_DATA = \
- 	features.gif					\
- 	flow_leftrightup.gif	flow_vrule.gif 		\
-diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.am gromacs-4.0.5/share/html/online/Makefile.am
---- gromacs-4.0.5.orig/share/html/online/Makefile.am	2008-08-11 11:46:17.000000000 +0200
-+++ gromacs-4.0.5/share/html/online/Makefile.am	2009-11-29 23:01:47.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--onlinedir = ${pkgdatadir}/html/online
-+onlinedir = @htmldir@/html/online
- 
- online_DATA = \
-   cpt.html	\
-diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.in gromacs-4.0.5/share/html/online/Makefile.in
---- gromacs-4.0.5.orig/share/html/online/Makefile.in	2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/online/Makefile.in	2009-11-29 23:02:15.000000000 +0100
-@@ -186,7 +186,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--onlinedir = ${pkgdatadir}/html/online
-+onlinedir = @htmldir@/html/online
- online_DATA = \
-   cpt.html	\
-   dat.html           g_disre.html      g_sorient.html        ndx.html        \
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.5-path-overflow.patch b/sci-chemistry/gromacs/files/gromacs-4.0.5-path-overflow.patch
deleted file mode 100644
index 8f723e38d..000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.5-path-overflow.patch
+++ /dev/null
@@ -1,122 +0,0 @@
-fixes bug #284431 taken from upstream stable banch
-
-From 53a07a791c1b7e4ed832ed4842928ad5139c1f41 Mon Sep 17 00:00:00 2001
-From: kasson <kasson>
-Date: Wed, 11 Mar 2009 11:19:09 +0000
-Subject: [PATCH] PK fixed buffer overruns in get_libdir(); some untested strcat() calls remain.
-
----
- src/gmxlib/futil.c |   31 ++++++++++++++++---------------
- 1 files changed, 16 insertions(+), 15 deletions(-)
-
-diff --git a/src/gmxlib/futil.c b/src/gmxlib/futil.c
-index e1b60cc..b83b2ea 100644
---- a/src/gmxlib/futil.c
-+++ b/src/gmxlib/futil.c
-@@ -52,6 +52,8 @@
- #include "smalloc.h"
- #include "statutil.h"
- 
-+#define MAX_PATHBUF 4096
-+
- typedef struct t_pstack {
-   FILE   *fp;
-   struct t_pstack *prev;
-@@ -385,20 +387,19 @@ static bool filename_is_absolute(char *name)
- #endif
- }
- 
--
- bool get_libdir(char *libdir)
- {
-   char bin_name[512];
-   char buf[512];
--  char full_path[512];
--  char test_file[512];
--  char system_path[512];
-+  char full_path[MAX_PATHBUF];
-+  char test_file[MAX_PATHBUF];
-+  char system_path[MAX_PATHBUF];
-   char *dir,*ptr,*s,*pdum;
-   bool found=FALSE;
-   int i;
- 
-   /* First - detect binary name */
--  strcpy(bin_name,Program());
-+  strncpy(bin_name,Program(),512);
-   
-   /* On windows & cygwin we need to add the .exe extension
-    * too, or we wont be able to detect that the file exists
-@@ -409,7 +410,7 @@ bool get_libdir(char *libdir)
- #endif
- 
-   /* Only do the smart search part if we got a real name */
--  if (NULL!=bin_name && strcmp(bin_name,"GROMACS")) {
-+  if (NULL!=bin_name && strncmp(bin_name,"GROMACS",512)) {
-   
-     if (!strchr(bin_name,DIR_SEPARATOR)) {
-       /* No slash or backslash in name means it must be in the path - search it! */
-@@ -435,11 +436,11 @@ bool get_libdir(char *libdir)
-        * name is relative to the current dir 
-        */
-       pdum=getcwd(buf,sizeof(buf)-1);
--      strcpy(full_path,buf);
-+      strncpy(full_path,buf,MAX_PATHBUF);
-       strcat(full_path,"/");
-       strcat(full_path,bin_name);
-     } else {
--      strcpy(full_path,bin_name);
-+      strncpy(full_path,bin_name,MAX_PATHBUF);
-     }
-     
-     /* Now we should have a full path and name in full_path,
-@@ -450,9 +451,9 @@ bool get_libdir(char *libdir)
-       buf[i]='\0';
-       /* If it doesn't start with "/" it is relative */
-       if (buf[0]!=DIR_SEPARATOR) {
--	strcpy(strrchr(full_path,DIR_SEPARATOR)+1,buf);
-+	strncpy(strrchr(full_path,DIR_SEPARATOR)+1,buf,MAX_PATHBUF);
-       } else
--	strcpy(full_path,buf);
-+	strncpy(full_path,buf,MAX_PATHBUF);
-     }
- #endif
-     
-@@ -489,10 +490,10 @@ const char *low_libfn(const char *file, bool bFatal)
-   const char *ret=NULL;
-   char *lib,*dir;
-   static char buf[1024];
--  static char libpath[4096];
-+  static char libpath[MAX_PATHBUF];
-   static int  bFirst=1;
-   static bool env_is_set;
--  char   *s,tmppath[4096];
-+  char   *s,tmppath[MAX_PATHBUF];
-   bool found;
-   
-   if (bFirst) {
-@@ -500,10 +501,10 @@ const char *low_libfn(const char *file, bool bFatal)
-     lib=getenv("GMXLIB");
-     if (lib != NULL) {
-       env_is_set=TRUE;
--      strcpy(libpath,lib);
-+      strncpy(libpath,lib,MAX_PATHBUF);
-     } 
-     else if (!get_libdir(libpath))
--      strcpy(libpath,GMXLIBDIR);
-+      strncpy(libpath,GMXLIBDIR,MAX_PATHBUF);
-     
-     bFirst=0;
-   }
-@@ -512,7 +513,7 @@ const char *low_libfn(const char *file, bool bFatal)
-     ret=file;
-   else {
-     found=FALSE;
--    strcpy(tmppath,libpath);
-+    strncpy(tmppath,libpath,MAX_PATHBUF);
-     s=tmppath;
-     while(!found && (dir=strtok(s,PATH_SEPARATOR))!=NULL) {
-       sprintf(buf,"%s%c%s",dir,DIR_SEPARATOR,file);
--- 
-1.6.5.GIT
-
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch
new file mode 100644
index 000000000..e32ddec90
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch
@@ -0,0 +1,36 @@
+diff -Naur gromacs-4.0.5.orig/share/html/Makefile.am gromacs-4.0.5/share/html/Makefile.am
+--- gromacs-4.0.5.orig/share/html/Makefile.am	2006-03-06 10:52:20.000000000 +0100
++++ gromacs-4.0.5/share/html/Makefile.am	2009-11-29 22:27:24.000000000 +0100
+@@ -4,7 +4,7 @@
+ #
+ SUBDIRS = .  images  online
+ 
+-htmldir = ${pkgdatadir}/html
++htmldir = @htmldir@/html
+ 
+ html_DATA = online.html gmxfaq.html
+ 
+diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.am gromacs-4.0.5/share/html/images/Makefile.am
+--- gromacs-4.0.5.orig/share/html/images/Makefile.am	2006-03-06 10:52:20.000000000 +0100
++++ gromacs-4.0.5/share/html/images/Makefile.am	2009-11-29 23:00:57.000000000 +0100
+@@ -2,7 +2,7 @@
+ #
+ # Don't edit - this file is generated automatically from Makefile.am
+ #
+-imagedir = ${pkgdatadir}/html/images
++imagedir = @htmldir@/html/images
+ 
+ image_DATA = \
+ 	features.gif					\
+diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.am gromacs-4.0.5/share/html/online/Makefile.am
+--- gromacs-4.0.5.orig/share/html/online/Makefile.am	2008-08-11 11:46:17.000000000 +0200
++++ gromacs-4.0.5/share/html/online/Makefile.am	2009-11-29 23:01:47.000000000 +0100
+@@ -2,7 +2,7 @@
+ #
+ # Don't edit - this file is generated automatically from Makefile.am
+ #
+-onlinedir = ${pkgdatadir}/html/online
++onlinedir = @htmldir@/html/online
+ 
+ online_DATA = \
+   cpt.html	\
diff --git a/sci-chemistry/gromacs/gromacs-3.3.9999.ebuild b/sci-chemistry/gromacs/gromacs-3.3.9999.ebuild
deleted file mode 100644
index 8d354932d..000000000
--- a/sci-chemistry/gromacs/gromacs-3.3.9999.ebuild
+++ /dev/null
@@ -1,234 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-inherit autotools bash-completion eutils fortran git multilib
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11 )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-EGIT_BRANCH="release-3-3-patches"
-
-src_prepare() {
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
-
-	eautoreconf
-
-	cd "${WORKDIR}"
-
-	use test && mv gmxtest "${P}"
-	mv "${P}" "${P}-single"
-	if ( use double-precision ) ; then
-		einfo "Moving sources for Multiprecision Build"
-		cp -prP "${P}-single" "${P}-double"
-	fi
-}
-
-src_configure() {
-	local myconf ;
-	local myconf_s ;
-	local myconf_d ;
-	local suffix_d ;
-
-	#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 [[ $(gcc-version) == "4.1" ]]; then
-		ewarn "gcc 4.1 is not supported by gromacs"
-		ewarn "please run test suite"
-	fi
-
-	#fortran will gone in gromacs 4.1 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-		FORTRAN="g77 gfortran ifc"
-		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-	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} $(use_with lapack external-lapack)"
-	fi
-
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--docdir=/usr/share/doc/"${PF}" \
-			$(use_with dmalloc) \
-			$(use_with fftw fft fftw3) \
-			$(use_with gsl) \
-			$(use_enable mpi) \
-			$(use_with X x) \
-			$(use_with xml) \
-			$(use_enable static all-static) \
-			${myconf}"
-
-	#if we build both double is suffixed
-	if ( use double-precision && use single-precision ); then
-		suffix_d="_d"
-	else
-		suffix_d=""
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required	to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-		einfo "Configuring Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
-		econf ${myconf_d} || die "Double Precision econf failed"
-	fi
-
-	if use single-precision ; then
-		einfo "Configuring Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --program-suffix=''"
-		econf ${myconf_s} || die "configure failed"
-	fi
-}
-
-src_compile() {
-	if use double-precision ; then
-		einfo "Building Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		emake || die "Double Precision emake failed"
-	fi
-
-	if use single-precision ; then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		emake || die "Single Precision emake failed"
-	fi
-}
-
-src_test() {
-	if use single-precision ; then
-		export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
-		cd "${WORKDIR}"/"${P}"-single
-		emake -j1 tests || die "Single Precision test failed"
-	fi
-
-	if use double-precision ; then
-		export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
-		cd "${WORKDIR}"/"${P}"-double
-		emake -j1 tests || die "Double Precision test failed"
-	fi
-}
-
-src_install() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${WORKDIR}"/"${P}"-single
-		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
-	fi
-
-	if use double-precision ; then
-		einfo "Installing Double Precision"
-		cd "${WORKDIR}"/"${P}"-double
-		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
-	fi
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	doenvd "${T}/80gromacs"
-	rm -f "${D}"/usr/bin/GMXRC*
-
-	dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${D}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -r "${D}"/usr/bin/completion.*
-
-	dodoc AUTHORS INSTALL README
-	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
-}
-
-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-4.0.4.ebuild b/sci-chemistry/gromacs/gromacs-4.0.4.ebuild
deleted file mode 100644
index 344302aee..000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.4.ebuild
+++ /dev/null
@@ -1,243 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.2.ebuild,v 1.1 2009/01/04 01:04:00 je_fro Exp $
-
-EAPI="2"
-
-LIBTOOLIZE="true"
-
-inherit autotools eutils flag-o-matic fortran multilib
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="3dnow X altivec blas double-precision gsl lapack gmxmopac7 mpi +single-precision sse sse2 static xml"
-
-# mopac7 qm/mm is broken until we can get files from
-# http://md.chem.rug.nl/~groenhof/qmmm.html
-# or somewhere else...
-
-DEPEND=">=sci-libs/fftw-3.0.1
-	app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libXt
-		x11-libs/libXp
-		x11-libs/libXext
-		x11-proto/xproto
-		x11-libs/openmotif )
-	blas? ( virtual/blas )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	gmxmopac7? ( sci-chemistry/mopac7[gmxmopac7=] )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran ifc"
-
-src_prepare() {
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	append-ldflags -Wl,--no-as-needed
-
-	eautoreconf
-
-	cd "${WORKDIR}"
-	mv "${P}" "${P}-single"
-	if ( use double-precision ) ; then
-		einfo "Moving sources for Multiprecision Build"
-		cp -prP "${P}-single" "${P}-double"
-	fi
-}
-
-src_configure() {
-
-	# static should work but something's broken.
-	# gcc spec file may be screwed up.
-	# Static linking should try -lgcc instead of -lgcc_s.
-	# For more info:
-	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-
-	# We will compile single precision by default, and suffix double-precision with _d.
-	# Sparc is the only arch I can test on that needs to use fortran.
-	local myconf ;
-	local myconf_s ;
-	local myconf_d ;
-
-	case "${ARCH}" in
-
-		x86)
-			if ( use sse || use sse2 ) ; then
-				myconf="${myconf} --enable-ia32-sse"
-			fi
-			myconf="$myconf $(use_enable 3dnow ia32-3dnow)"
-
-			if ( ! use sse && ! use sse2 && ! use 3dnow ) ; then
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-				fi
-			else
-				myconf="${myconf} --disable-fortran"
-			fi
-			;;
-
-		amd64)
-			myconf="$myconf --enable-x86-64-sse --disable-fortran"
-			;;
-
-		ppc*)
-			if use altivec ; then
-				myconf="${myconf} --enable-ppc-altivec --disable-fortran"
-			else
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-				fi
-			fi
-			;;
-
-		ia64)
-			myconf="$myconf --enable-ia64-asm --disable-fortran"
-			;;
-
-		alpha)
-			if ! has_version "=sys-devel/gcc-3*" ; then
-				die "If you must run gromacs without sse (not recommended) gfortran will not work."
-			else
-				myconf="$myconf --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-
-		sparc)
-			if ! has_version "=sys-devel/gcc-3*" ; then
-				die "If you must run gromacs without sse (not recommended) gfortran will not work."
-			else
-				myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-	esac
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${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} $(use_with lapack external-lapack)"
-	fi
-	if use gmxmopac7; then
-		export LIBS="${LIBS} -lgmxmopac7"
-		myconf="${myconf} $(use_with gmxmopac7 qmmm-mopac)"
-	fi
-	# by default gromacs builds as static since 4.0.3
-	if use static; then
-		myconf="${myconf} --enable-all-static"
-	else
-		myconf="${myconf} --enable-shared"
-	fi
-
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--with-fft=fftw3 \
-			$(use_with gsl) \
-			$(use_enable mpi) \
-			$(use_with X x) \
-			$(use_with xml) \
-			${myconf}"
-
-	if ( use double-precision && use single-precision ); then
-		einfo "Configuring Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf}  --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "Single Precision econf failed"
-
-		einfo "Configuring Double Precision Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=_d"
-		econf ${myconf_d} || die "Double Precision econf failed"
-
-	elif use double-precision ; then
-		einfo "Configuring Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=''"
-		econf ${myconf_d} || die "Double Precision econf failed"
-
-	elif use single-precision ; then
-		einfo "Configuring Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "configure failed"
-	fi
-}
-
-src_compile() {
-	if ( use double-precision && use single-precision ); then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		emake || die "Single Precision emake failed"
-
-		einfo "Building Double Precision Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		emake || die "Double Precision emake failed"
-
-	elif use double-precision ; then
-		einfo "Building Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		emake || die "Double Precision emake failed"
-
-	elif use single-precision ; then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		emake || die "Single Precision emake failed"
-	fi
-}
-
-src_install() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${WORKDIR}"/"${P}"-single
-		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
-	fi
-
-	if use double-precision ; then
-		einfo "Installing Double Precision"
-		cd "${WORKDIR}"/"${P}"-double
-		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
-	fi
-
-	dodoc AUTHORS INSTALL README
-	# Move html and leave examples and templates under /usr/share/gromacs.
-	mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.0.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.0.5-r1.ebuild
deleted file mode 100644
index 21c2bd1b7..000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.5-r1.ebuild
+++ /dev/null
@@ -1,237 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-inherit autotools bash-completion eutils fortran multilib
-
-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-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-src_prepare() {
-
-	epatch "${FILESDIR}/${PN}-4.0.4-sparc-cyclecounter.patch"
-	epatch "${FILESDIR}/${P}-path-overflow.patch"
-	epatch "${FILESDIR}/${P}-docdir.patch"
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
-
-	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 [[ $(gcc-version) == "4.1" ]]; then
-		ewarn "gcc 4.1 is not supported by gromacs"
-		ewarn "please run test suite"
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 4.1 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-		FORTRAN="g77 gfortran ifc"
-		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-	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} $(use_with lapack external-lapack)"
-	fi
-
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--docdir=/usr/share/doc/"${PF}" \
-			$(use_with dmalloc) \
-			$(use_with fftw fft fftw3) \
-			$(use_with gsl) \
-			$(use_with X x) \
-			$(use_with xml) \
-			$(use_enable static all-static) \
-			${myconf}"
-
-	#if we build single and double - double is suffixed
-	if ( use double-precision && use single-precision ); then
-		suffixdouble="_d"
-	else
-		suffixdouble=""
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	myconfdouble="${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 ${!p} --disable-mpi
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
-	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 ${x} failed"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	doenvd "${T}/80gromacs"
-	rm -f "${D}"/usr/bin/GMXRC*
-
-	dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${D}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -r "${D}"/usr/bin/completion.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL README
-	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
-}
-
-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-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
index 63fd0da23..ca1ee7a21 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -7,7 +7,7 @@ EAPI="2"
 LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 
-inherit autotools bash-completion eutils fortran git multilib
+inherit autotools bash-completion eutils flag-o-matic fortran git multilib
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -17,10 +17,12 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
 
 DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11 )
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
 	dmalloc? ( dev-libs/dmalloc )
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
@@ -37,6 +39,8 @@ EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 EGIT_BRANCH="release-4-0-patches"
 
 src_prepare() {
+
+	epatch "${FILESDIR}/${P}-docdir.patch"
 	# Fix typos in a couple of files.
 	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
 		|| die "Failed to fixup demo script."
@@ -60,23 +64,25 @@ src_prepare() {
 
 	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
 
+	append-ldflags -Wl,--no-as-needed
 	eautoreconf
 
-	cd "${WORKDIR}"
-
-	use test && mv gmxtest "${P}"
-	mv "${P}" "${P}-single"
-	if ( use double-precision ) ; then
-		einfo "Moving sources for Multiprecision Build"
-		cp -prP "${P}-single" "${P}-double"
-	fi
+	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 myconf_s ;
-	local myconf_d ;
-	local suffix_d ;
+	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!
@@ -90,10 +96,13 @@ src_configure() {
 	fi
 
 	if [[ $(gcc-version) == "4.1" ]]; then
-		ewarn "gcc 4.1 is not supported by gromacs"
-		ewarn "please run test suite"
+		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
@@ -117,6 +126,13 @@ src_configure() {
 		myconf="${myconf} $(use_with lapack external-lapack)"
 	fi
 
+	# by default its better to have dynamicaly linked binaries
+	if use static; then
+		myconf="${myconf} $(use_enable static all-static)"
+	else
+		myconf="${myconf} --enable-shared"
+	fi
+
 	myconf="--datadir=/usr/share \
 			--bindir=/usr/bin \
 			--libdir=/usr/$(get_libdir) \
@@ -124,24 +140,22 @@ src_configure() {
 			$(use_with dmalloc) \
 			$(use_with fftw fft fftw3) \
 			$(use_with gsl) \
-			$(use_enable mpi) \
 			$(use_with X x) \
 			$(use_with xml) \
-			$(use_enable static all-static) \
 			${myconf}"
 
-	#if we build both double is suffixed
+	#if we build single and double - double is suffixed
 	if ( use double-precision && use single-precision ); then
-		suffix_d="_d"
+		suffixdouble="_d"
 	else
-		suffix_d=""
+		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 "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 "
@@ -149,60 +163,57 @@ src_configure() {
 		elog "-energy conservation: this can only be done without temperature coupling and"
 		elog " without cutoffs"
 		elog
-		einfo "Configuring Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
-		econf ${myconf_d} || die "Double Precision econf failed"
 	fi
 
-	if use single-precision ; then
-		einfo "Configuring Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --program-suffix=''"
-		econf ${myconf_s} || die "configure failed"
-	fi
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	myconfdouble="${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 ${!p} --disable-mpi
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
+	done
 }
 
 src_compile() {
-	if use double-precision ; then
-		einfo "Building Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		emake || die "Double Precision emake failed"
-	fi
-
-	if use single-precision ; then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		emake || die "Single Precision emake failed"
-	fi
+	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() {
-	if use single-precision ; then
-		export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
-		cd "${WORKDIR}"/"${P}"-single
-		emake -j1 tests || die "Single Precision test failed"
-	fi
-
-	if use double-precision ; then
-		export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
-		cd "${WORKDIR}"/"${P}"-double
-		emake -j1 tests || die "Double Precision test failed"
-	fi
+	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() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${WORKDIR}"/"${P}"-single
-		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
-	fi
-
-	if use double-precision ; then
-		einfo "Installing Double Precision"
-		cd "${WORKDIR}"/"${P}"-double
-		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
-	fi
+	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' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
 	doenvd "${T}/80gromacs"
@@ -215,6 +226,7 @@ src_install() {
 	fi
 	rm -r "${D}"/usr/bin/completion.*
 
+	cd "${S}"
 	dodoc AUTHORS INSTALL README
 	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
 }
@@ -223,12 +235,12 @@ pkg_postinst() {
 	env-update && source /etc/profile
 	elog
 	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 \(2008\). "
+	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 "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
 	elog
 }
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index e8384fb66..a13a611f4 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -7,7 +7,7 @@ EAPI="2"
 LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 
-inherit autotools bash-completion eutils fortran git multilib
+inherit autotools bash-completion eutils flag-o-matic fortran git multilib
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -17,10 +17,12 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
 
 DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11 )
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
 	dmalloc? ( dev-libs/dmalloc )
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
@@ -34,8 +36,11 @@ RDEPEND="${DEPEND}"
 RESTRICT="test"
 
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+EGIT_BRANCH="master"
 
 src_prepare() {
+
+	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
 	# Fix typos in a couple of files.
 	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
 		|| die "Failed to fixup demo script."
@@ -59,23 +64,25 @@ src_prepare() {
 
 	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
 
+	append-ldflags -Wl,--no-as-needed
 	eautoreconf
 
-	cd "${WORKDIR}"
-
-	use test && mv gmxtest "${P}"
-	mv "${P}" "${P}-single"
-	if ( use double-precision ) ; then
-		einfo "Moving sources for Multiprecision Build"
-		cp -prP "${P}-single" "${P}-double"
-	fi
+	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 myconf_s ;
-	local myconf_d ;
-	local suffix_d ;
+	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!
@@ -89,10 +96,13 @@ src_configure() {
 	fi
 
 	if [[ $(gcc-version) == "4.1" ]]; then
-		ewarn "gcc 4.1 is not supported by gromacs"
-		ewarn "please run test suite"
+		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
@@ -116,6 +126,13 @@ src_configure() {
 		myconf="${myconf} $(use_with lapack external-lapack)"
 	fi
 
+	# by default its better to have dynamicaly linked binaries
+	if use static; then
+		myconf="${myconf} $(use_enable static all-static)"
+	else
+		myconf="${myconf} --enable-shared"
+	fi
+
 	myconf="--datadir=/usr/share \
 			--bindir=/usr/bin \
 			--libdir=/usr/$(get_libdir) \
@@ -123,24 +140,22 @@ src_configure() {
 			$(use_with dmalloc) \
 			$(use_with fftw fft fftw3) \
 			$(use_with gsl) \
-			$(use_enable mpi) \
 			$(use_with X x) \
 			$(use_with xml) \
-			$(use_enable static all-static) \
 			${myconf}"
 
-	#if we build both double is suffixed
+	#if we build single and double - double is suffixed
 	if ( use double-precision && use single-precision ); then
-		suffix_d="_d"
+		suffixdouble="_d"
 	else
-		suffix_d=""
+		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 "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 "
@@ -148,60 +163,57 @@ src_configure() {
 		elog "-energy conservation: this can only be done without temperature coupling and"
 		elog " without cutoffs"
 		elog
-		einfo "Configuring Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
-		econf ${myconf_d} || die "Double Precision econf failed"
 	fi
 
-	if use single-precision ; then
-		einfo "Configuring Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --program-suffix=''"
-		econf ${myconf_s} || die "configure failed"
-	fi
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	myconfdouble="${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 ${!p} --disable-mpi
+		use mpi || continue
+		cd "${S}-${x}_mpi"
+		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
+	done
 }
 
 src_compile() {
-	if use double-precision ; then
-		einfo "Building Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		emake || die "Double Precision emake failed"
-	fi
-
-	if use single-precision ; then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		emake || die "Single Precision emake failed"
-	fi
+	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() {
-	if use single-precision ; then
-		export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
-		cd "${WORKDIR}"/"${P}"-single
-		emake -j1 tests || die "Single Precision test failed"
-	fi
-
-	if use double-precision ; then
-		export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
-		cd "${WORKDIR}"/"${P}"-double
-		emake -j1 tests || die "Double Precision test failed"
-	fi
+	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() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${WORKDIR}"/"${P}"-single
-		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
-	fi
-
-	if use double-precision ; then
-		einfo "Installing Double Precision"
-		cd "${WORKDIR}"/"${P}"-double
-		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
-	fi
+	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' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
 	doenvd "${T}/80gromacs"
@@ -214,6 +226,7 @@ src_install() {
 	fi
 	rm -r "${D}"/usr/bin/completion.*
 
+	cd "${S}"
 	dodoc AUTHORS INSTALL README
 	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
 }
@@ -222,12 +235,12 @@ pkg_postinst() {
 	env-update && source /etc/profile
 	elog
 	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 \(2008\). "
+	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 "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
 	elog
 }
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8f140cfbf..ffe0affee 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -8,7 +8,6 @@
   <flag name='fkernels'>Enable building of Fortran Kernels for platforms
 	  that dont have assembly loops</flag>
   <flag name='single-precision'>Single precision version of gromacs</flag>
-  <flag name='gmxmopac7'>Support for QM/MM with mopac7</flag>
   <flag name='zsh-completion'>Enable zsh completion support</flag>
 </use>
 </pkgmetadata>