Tue Nov 23 19:43:59 2010 UTC ()
Update to Gromacs 4.5.3

This is maintainance release, it fixes:

* Double precision energy file reading
* CHARMM and GB issues
* Support for Altivec (PowerPC) with CMake
* Running binaries within the CMake build tree is now possible
* Various other issues


(asau)
diff -r1.5 -r1.6 pkgsrc/biology/gromacs/Makefile
diff -r1.4 -r1.5 pkgsrc/biology/gromacs/PLIST
diff -r1.6 -r1.7 pkgsrc/biology/gromacs/distinfo
cvs diff -r1.5 -r1.6 pkgsrc/biology/gromacs/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/gromacs/Makefile 2010/10/21 12:03:57 1.5
+++ pkgsrc/biology/gromacs/Makefile 2010/11/23 19:43:58 1.6
@@ -1,34 +1,27 @@ @@ -1,34 +1,27 @@
1# $NetBSD: Makefile,v 1.5 2010/10/21 12:03:57 asau Exp $ 1# $NetBSD: Makefile,v 1.6 2010/11/23 19:43:58 asau Exp $
2# 2#
3 3
4DISTNAME= gromacs-4.5.1 4DISTNAME= gromacs-4.5.3
5PKGNAME= $(DISTNAME:=.1) 
6CATEGORIES= biology 5CATEGORIES= biology
7MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ 6MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/
8 7
9MAINTAINER= pkgsrc-users@NetBSD.org 8MAINTAINER= pkgsrc-users@NetBSD.org
10HOMEPAGE= http://www.gromacs.org/ 9HOMEPAGE= http://www.gromacs.org/
11COMMENT= Molecular dynamics package 10COMMENT= Molecular dynamics package
12LICENSE= gnu-gpl-v2 11LICENSE= gnu-gpl-v2
13 12
14PKG_DESTDIR_SUPPORT= user-destdir 13PKG_DESTDIR_SUPPORT= user-destdir
15 14
16# GROMACS team released another version a day after: 
17# 4.5.1-20100902-2d7e855 vs. 
18# 4.5.1-20100903-d982058 
19# call it 4.5.1.1 
20DIST_SUBDIR= gromacs-4.5.1.1 
21 
22# Official recommendation is not to use the gcc 4.1.x set of compilers. 15# Official recommendation is not to use the gcc 4.1.x set of compilers.
23 16
24GNU_CONFIGURE= yes 17GNU_CONFIGURE= yes
25USE_LIBTOOL= yes 18USE_LIBTOOL= yes
26USE_PKGLOCALEDIR= yes 19USE_PKGLOCALEDIR= yes
27USE_TOOLS+= pkg-config 20USE_TOOLS+= pkg-config
28 21
29CONFIGURE_ARGS+= --enable-shared 22CONFIGURE_ARGS+= --enable-shared
30CONFIGURE_ARGS+= --enable-double --program-suffix= 23CONFIGURE_ARGS+= --enable-double --program-suffix=
31CONFIGURE_ARGS+= --with-gsl 24CONFIGURE_ARGS+= --with-gsl
32CONFIGURE_ARGS+= --disable-gcc41-check 25CONFIGURE_ARGS+= --disable-gcc41-check
33 26
34.include "options.mk" 27.include "options.mk"
cvs diff -r1.4 -r1.5 pkgsrc/biology/gromacs/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/gromacs/PLIST 2010/10/21 12:03:57 1.4
+++ pkgsrc/biology/gromacs/PLIST 2010/11/23 19:43:58 1.5
@@ -1,14 +1,14 @@ @@ -1,14 +1,14 @@
1@comment $NetBSD: PLIST,v 1.4 2010/10/21 12:03:57 asau Exp $ 1@comment $NetBSD: PLIST,v 1.5 2010/11/23 19:43:58 asau Exp $
2bin/GMXRC 2bin/GMXRC
3bin/GMXRC.bash 3bin/GMXRC.bash
4bin/GMXRC.csh 4bin/GMXRC.csh
5bin/GMXRC.zsh 5bin/GMXRC.zsh
6bin/completion.bash 6bin/completion.bash
7bin/completion.csh 7bin/completion.csh
8bin/completion.zsh 8bin/completion.zsh
9bin/demux.pl 9bin/demux.pl
10bin/do_dssp 10bin/do_dssp
11bin/editconf 11bin/editconf
12bin/eneconv 12bin/eneconv
13bin/g_anadock 13bin/g_anadock
14bin/g_anaeig 14bin/g_anaeig
@@ -29,26 +29,27 @@ bin/g_dielectric @@ -29,26 +29,27 @@ bin/g_dielectric
29bin/g_dih 29bin/g_dih
30bin/g_dipoles 30bin/g_dipoles
31bin/g_disre 31bin/g_disre
32bin/g_dist 32bin/g_dist
33bin/g_dyndom 33bin/g_dyndom
34bin/g_enemat 34bin/g_enemat
35bin/g_energy 35bin/g_energy
36bin/g_filter 36bin/g_filter
37bin/g_gyrate 37bin/g_gyrate
38bin/g_h2order 38bin/g_h2order
39bin/g_hbond 39bin/g_hbond
40bin/g_helix 40bin/g_helix
41bin/g_helixorient 41bin/g_helixorient
 42bin/g_kinetics
42bin/g_lie 43bin/g_lie
43bin/g_luck 44bin/g_luck
44bin/g_mdmat 45bin/g_mdmat
45bin/g_membed 46bin/g_membed
46bin/g_mindist 47bin/g_mindist
47bin/g_morph 48bin/g_morph
48bin/g_msd 49bin/g_msd
49bin/g_nmeig 50bin/g_nmeig
50bin/g_nmens 51bin/g_nmens
51bin/g_nmtraj 52bin/g_nmtraj
52bin/g_order 53bin/g_order
53bin/g_pme_error 54bin/g_pme_error
54bin/g_polystat 55bin/g_polystat
@@ -771,42 +772,52 @@ share/gromacs/top/atommass.dat @@ -771,42 +772,52 @@ share/gromacs/top/atommass.dat
771share/gromacs/top/bonds.dlg 772share/gromacs/top/bonds.dlg
772share/gromacs/top/bromacs.dat 773share/gromacs/top/bromacs.dat
773share/gromacs/top/ca-shift.dat 774share/gromacs/top/ca-shift.dat
774share/gromacs/top/cb-shift.dat 775share/gromacs/top/cb-shift.dat
775share/gromacs/top/charmm27.ff/aminoacids.arn 776share/gromacs/top/charmm27.ff/aminoacids.arn
776share/gromacs/top/charmm27.ff/aminoacids.c.tdb 777share/gromacs/top/charmm27.ff/aminoacids.c.tdb
777share/gromacs/top/charmm27.ff/aminoacids.hdb 778share/gromacs/top/charmm27.ff/aminoacids.hdb
778share/gromacs/top/charmm27.ff/aminoacids.n.tdb 779share/gromacs/top/charmm27.ff/aminoacids.n.tdb
779share/gromacs/top/charmm27.ff/aminoacids.r2b 780share/gromacs/top/charmm27.ff/aminoacids.r2b
780share/gromacs/top/charmm27.ff/aminoacids.rtp 781share/gromacs/top/charmm27.ff/aminoacids.rtp
781share/gromacs/top/charmm27.ff/aminoacids.vsd 782share/gromacs/top/charmm27.ff/aminoacids.vsd
782share/gromacs/top/charmm27.ff/atomtypes.atp 783share/gromacs/top/charmm27.ff/atomtypes.atp
783share/gromacs/top/charmm27.ff/cmap.itp 784share/gromacs/top/charmm27.ff/cmap.itp
 785share/gromacs/top/charmm27.ff/dna.arn
 786share/gromacs/top/charmm27.ff/dna.c.tdb
 787share/gromacs/top/charmm27.ff/dna.hdb
 788share/gromacs/top/charmm27.ff/dna.n.tdb
784share/gromacs/top/charmm27.ff/dna.rtp 789share/gromacs/top/charmm27.ff/dna.rtp
785share/gromacs/top/charmm27.ff/ffbonded.itp 790share/gromacs/top/charmm27.ff/ffbonded.itp
786share/gromacs/top/charmm27.ff/ffnabonded.itp 791share/gromacs/top/charmm27.ff/ffnabonded.itp
787share/gromacs/top/charmm27.ff/ffnanonbonded.itp 792share/gromacs/top/charmm27.ff/ffnanonbonded.itp
788share/gromacs/top/charmm27.ff/ffnonbonded.itp 793share/gromacs/top/charmm27.ff/ffnonbonded.itp
789share/gromacs/top/charmm27.ff/forcefield.doc 794share/gromacs/top/charmm27.ff/forcefield.doc
790share/gromacs/top/charmm27.ff/forcefield.itp 795share/gromacs/top/charmm27.ff/forcefield.itp
791share/gromacs/top/charmm27.ff/gb.itp 796share/gromacs/top/charmm27.ff/gb.itp
792share/gromacs/top/charmm27.ff/ions.itp 797share/gromacs/top/charmm27.ff/ions.itp
793share/gromacs/top/charmm27.ff/lipids.hdb 798share/gromacs/top/charmm27.ff/lipids.hdb
794share/gromacs/top/charmm27.ff/lipids.rtp 799share/gromacs/top/charmm27.ff/lipids.rtp
 800share/gromacs/top/charmm27.ff/rna.arn
 801share/gromacs/top/charmm27.ff/rna.c.tdb
 802share/gromacs/top/charmm27.ff/rna.hdb
 803share/gromacs/top/charmm27.ff/rna.n.tdb
 804share/gromacs/top/charmm27.ff/rna.r2b
795share/gromacs/top/charmm27.ff/rna.rtp 805share/gromacs/top/charmm27.ff/rna.rtp
796share/gromacs/top/charmm27.ff/spc.itp 806share/gromacs/top/charmm27.ff/spc.itp
797share/gromacs/top/charmm27.ff/spce.itp 807share/gromacs/top/charmm27.ff/spce.itp
798share/gromacs/top/charmm27.ff/tip3p.itp 808share/gromacs/top/charmm27.ff/tip3p.itp
799share/gromacs/top/charmm27.ff/tip4p.itp 809share/gromacs/top/charmm27.ff/tip4p.itp
 810share/gromacs/top/charmm27.ff/tip5p.itp
800share/gromacs/top/charmm27.ff/tips3p.itp 811share/gromacs/top/charmm27.ff/tips3p.itp
801share/gromacs/top/charmm27.ff/watermodels.dat 812share/gromacs/top/charmm27.ff/watermodels.dat
802share/gromacs/top/co-shift.dat 813share/gromacs/top/co-shift.dat
803share/gromacs/top/defselection.dat 814share/gromacs/top/defselection.dat
804share/gromacs/top/dgsolv.dat 815share/gromacs/top/dgsolv.dat
805share/gromacs/top/edissoc.dat 816share/gromacs/top/edissoc.dat
806share/gromacs/top/electroneg.dat 817share/gromacs/top/electroneg.dat
807share/gromacs/top/elements.dat 818share/gromacs/top/elements.dat
808share/gromacs/top/encads.ff/aminoacids.c.tdb 819share/gromacs/top/encads.ff/aminoacids.c.tdb
809share/gromacs/top/encads.ff/aminoacids.hdb 820share/gromacs/top/encads.ff/aminoacids.hdb
810share/gromacs/top/encads.ff/aminoacids.n.tdb 821share/gromacs/top/encads.ff/aminoacids.n.tdb
811share/gromacs/top/encads.ff/aminoacids.r2b 822share/gromacs/top/encads.ff/aminoacids.r2b
812share/gromacs/top/encads.ff/aminoacids.rtp 823share/gromacs/top/encads.ff/aminoacids.rtp
cvs diff -r1.6 -r1.7 pkgsrc/biology/gromacs/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/gromacs/distinfo 2010/10/21 12:03:57 1.6
+++ pkgsrc/biology/gromacs/distinfo 2010/11/23 19:43:58 1.7
@@ -1,12 +1,12 @@ @@ -1,12 +1,12 @@
1$NetBSD: distinfo,v 1.6 2010/10/21 12:03:57 asau Exp $ 1$NetBSD: distinfo,v 1.7 2010/11/23 19:43:58 asau Exp $
2 2
3SHA1 (gromacs-4.5.1.1/gromacs-4.5.1.tar.gz) = cbe52c3ec613fe8b652cd24b86c4fdf31b58c71b 3SHA1 (gromacs-4.5.3.tar.gz) = c4845e5e62d1f53ee443301dad00138feba6d275
4RMD160 (gromacs-4.5.1.1/gromacs-4.5.1.tar.gz) = 116ca5bc4644d1460086cfb2097961abd11db63b 4RMD160 (gromacs-4.5.3.tar.gz) = 2bb9cab3c611b93c4323e16b0d171c16cd407bf1
5Size (gromacs-4.5.1.1/gromacs-4.5.1.tar.gz) = 10304547 bytes 5Size (gromacs-4.5.3.tar.gz) = 10338471 bytes
6SHA1 (patch-aa) = 29c6683c71989621f0f41682b1c225f524a2d84f 6SHA1 (patch-aa) = 29c6683c71989621f0f41682b1c225f524a2d84f
7SHA1 (patch-ad) = 68b37154ba466e28cad0e539e25253c901421aaa 7SHA1 (patch-ad) = 68b37154ba466e28cad0e539e25253c901421aaa
8SHA1 (patch-ae) = 59a5e88abeee883483b557cab1681c9a9098870f 8SHA1 (patch-ae) = 59a5e88abeee883483b557cab1681c9a9098870f
9SHA1 (patch-ag) = 810d58d3ad787c9508f775674541775245402596 9SHA1 (patch-ag) = 810d58d3ad787c9508f775674541775245402596
10SHA1 (patch-ah) = 36ceeb409e59d8d3f0abe3bfa3ea3108f61f7a8e 10SHA1 (patch-ah) = 36ceeb409e59d8d3f0abe3bfa3ea3108f61f7a8e
11SHA1 (patch-ai) = ed4aa71eb56d1300c67cd17057f72ea452739f3d 11SHA1 (patch-ai) = ed4aa71eb56d1300c67cd17057f72ea452739f3d
12SHA1 (patch-aj) = 080d2923d729ff00de0f2cae75a82ec6c3769d6c 12SHA1 (patch-aj) = 080d2923d729ff00de0f2cae75a82ec6c3769d6c