From 3de31939271b46eb40e2e7eb790e8fe03589b8a5 Mon Sep 17 00:00:00 2001 From: Jussi Lehtola Date: Nov 01 2010 13:06:13 +0000 Subject: Update to 4.5.2. --- diff --git a/.gitignore b/.gitignore index 3705c33..cb1b3cd 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ gromacs-4.0.7.tar.gz manual-4.0.pdf /manual-4.5.pdf /gromacs-4.5.1.tar.gz +/gromacs-4.5.2.tar.gz diff --git a/gromacs-configure.patch b/gromacs-configure.patch deleted file mode 100644 index 945e5bc..0000000 --- a/gromacs-configure.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff -up gromacs-4.0.5/configure.orig gromacs-4.0.5/configure ---- gromacs-4.0.5/configure.orig 2009-05-22 11:59:34.000000000 +0300 -+++ gromacs-4.0.5/configure 2009-05-22 12:00:14.000000000 +0300 -@@ -31508,12 +31508,7 @@ AS="$CC" - # However, the non-suffixed names are linked to the _mpi and/or _d suffixed - # ones upon installation if that is the only version available. - --if test "$enable_mpi" = "yes"; then -- LIBSUFFIX="_mpi" --fi --if test "$enable_float" = "no"; then -- LIBSUFFIX="${LIBSUFFIX}_d" --fi -+LIBSUFFIX="@LIBSUFFIX@" - - - # Unless the user has explicitly requested a prefix/suffix/transform, we diff --git a/gromacs-gmxdemo.patch b/gromacs-gmxdemo.patch index 7160fb2..f146ab7 100644 --- a/gromacs-gmxdemo.patch +++ b/gromacs-gmxdemo.patch @@ -1,106 +1,315 @@ -diff -up gromacs-4.0.3/share/tutor/gmxdemo/demo.orig gromacs-4.0.3/share/tutor/gmxdemo/demo ---- gromacs-4.0.3/share/tutor/gmxdemo/demo.orig 2006-02-15 23:48:34.000000000 +0200 -+++ gromacs-4.0.3/share/tutor/gmxdemo/demo 2009-01-19 16:52:35.000000000 +0200 -@@ -80,9 +80,9 @@ set ans = $< +diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tutor/gmxdemo/demo +--- gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo 2010-09-29 14:35:03.000000000 +0300 ++++ gromacs-4.5.2/share/tutor/gmxdemo/demo 2010-11-01 14:04:34.833273502 +0200 +@@ -58,10 +58,10 @@ cat << _EOF_ + ----------------------------------------------------------------- + Before we can start any simulation we need a molecular toplogy + file. This topology file ( .top extension ) is generated by the +-program pdb2gmx. The only input file of the pdb2gmx program is the pdb ++program g_pdb2gmx. The only input file of the g_pdb2gmx program is the pdb + file of our peptide ( .pdb extension ). - echo "Starting pdb2gmx" +-Because most pdb files do not contain all hydrogen atoms, the pdb2gmx ++Because most pdb files do not contain all hydrogen atoms, the g_pdb2gmx + program will also add them to our peptide. The output file which + contains the structure of the peptide when hydrogen atoms are added is a + gromos structure file ( .gro extension ) +@@ -72,22 +72,22 @@ _EOF_ + + if ( $?DISPLAY ) then + echo "You seem to have the DISPLAY variable is set, so we will" +- echo "pop up a window with the output of the pdb2gmx program" ++ echo "pop up a window with the output of the g_pdb2gmx program" + endif + echo -n "Press " + set ans = $< + + +-echo "Starting pdb2gmx" ++echo "Starting g_pdb2gmx" if ( $?DISPLAY ) then - xterm -title pdb2gmx -sb -e tail +0f output.pdb2gmx & -+ xterm -title g_pdb2gmx -sb -e tail +0f output.pdb2gmx & ++ xterm -title g_pdb2gmx -sb -e tail +0f output.g_pdb2gmx & + endif +-pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx << KOKO ++g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.g_pdb2gmx << KOKO + 1 + 1 + KOKO + +-echo "pdb2gmx finished" ++echo "g_pdb2gmx finished" + echo -n "Press " + set ans = $< + +@@ -99,14 +99,14 @@ cat << _EOF_ + ----------------------------------------------------------------- + ----------------------------------------------------------------- + Because a simulation of a peptide in vacua is a bit unrealistic, we +-have to solvate our peptide in a box of water. genbox is the program ++have to solvate our peptide in a box of water. g_genbox is the program + we use to do this. + +-The genbox program reads the peptide structure file and an input file +-containing the sizes of the desired water box. The output of genbox is ++The g_genbox program reads the peptide structure file and an input file ++containing the sizes of the desired water box. The output of g_genbox is + a gromos structure file of a peptide solvated in a box of water. The +-genbox program also changes the topology file ( .top extension ) to +-include water. First we will use the program editconf to define the ++g_genbox program also changes the topology file ( .top extension ) to ++include water. First we will use the program g_editconf to define the + right boxsize for our system. + + ----------------------------------------------------------------- +@@ -114,22 +114,22 @@ right boxsize for our system. + _EOF_ + + if ( $?DISPLAY ) then +- echo "The output of the genbox program should appear" ++ echo "The output of the g_genbox program should appear" + echo "in a separate xterm window" endif --echo 0 | pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx -+echo 0 | g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx - echo "pdb2gmx finished" + echo -n "Press " set ans = $< -@@ -119,11 +119,11 @@ set ans = $< - echo "Starting editconf and genbox..." +-echo "Starting editconf and genbox..." ++echo "Starting g_editconf and g_genbox..." if ( $?DISPLAY ) then - xterm -title genbox -sb -e tail +0f output.genbox & -+ xterm -title g_genbox -sb -e tail +0f output.genbox & ++ xterm -title g_genbox -sb -e tail +0f output.g_genbox & endif -editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.genbox -+g_editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.genbox ++g_editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.g_genbox -genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.genbox -+g_genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.genbox ++g_genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.g_genbox - echo "editconf and genbox finished" +-echo "editconf and genbox finished" ++echo "g_editconf and g_genbox finished" echo -n "Press " -@@ -189,9 +189,9 @@ _EOF_ + set ans = $< - echo "Starting grompp..." +@@ -142,7 +142,7 @@ cat << _EOF_ + ----------------------------------------------------------------- + In principle we can start a Molecular Dynamics simulation now. However + it is not very wise to do so, because our system is full of close +-contacts. These close contacts are mainly a result of the genbox ++contacts. These close contacts are mainly a result of the g_genbox + program. The added solvent might have some close contacts with the + peptide resulting in very high repulsive energies. If we would start a + Molecular Dynamics (MD) simulation without energy minimisation the +@@ -153,7 +153,7 @@ Energy Minimisation (EM). Energy minimis + coordinates of our system to remove high energies from our system. + + Before we can start the Energy Minimisation we have to preprocess all +-the input files with the GROMACS preprocessor named grompp. grompp ++the input files with the GROMACS preprocessor named g_g_grompp. g_g_grompp + preprocesses the topology file (.top), the structure file (.gro) and a + parameter file (.mdp) resulting in a binary topology file (.tpr + extension). This binary topology file contains all information for a +@@ -163,7 +163,7 @@ simulation (in this case an energy minim + _EOF_ + + if ( $?DISPLAY ) then +- echo "The output of the grompp program should appear" ++ echo "The output of the g_g_grompp program should appear" + echo "in a separate xterm window" + endif + +@@ -191,13 +191,13 @@ emtol = 1000.0 + emstep = 0.01 + _EOF_ + +-echo "Starting grompp..." ++echo "Starting g_grompp..." if ( $?DISPLAY ) then - xterm -title grompp -sb -e tail +0f output.grompp_em & -+ xterm -title g_grompp -sb -e tail +0f output.grompp_em & ++ xterm -title g_grompp -sb -e tail +0f output.g_grompp_em & endif -grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em -+g_grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em ++g_grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.g_grompp_em - echo "grompp finished" +-echo "grompp finished" ++echo "g_grompp finished" echo -n "Press " -@@ -230,9 +230,9 @@ set ans = $< - echo "starting energy minimisation mdrun..." + set ans = $< + +@@ -210,8 +210,8 @@ cat << _EOF_ + ----------------------------------------------------------------- + Now the binary topology file is generated, we can start the energy + minimisation (EM). The program which performs the EM is called +-mdrun. In fact all simulations are performed by the same program: +-mdrun. ++g_mdrun. In fact all simulations are performed by the same program: ++g_mdrun. + + As the Energy Minimisation is running, watch the output of the + program. The first number ( from left to right ) is the number of the +@@ -224,21 +224,21 @@ rapidly drops down, and converges, to a + _EOF_ + + if ( $?DISPLAY ) then +- echo "The output of the mdrun program should appear" ++ echo "The output of the g_mdrun program should appear" + echo "in a separate xterm window" + endif + + echo -n "Press " + set ans = $< + +-echo "starting energy minimisation mdrun..." ++echo "starting energy minimisation g_mdrun..." if ( $?DISPLAY ) then - xterm -title mdrun -sb -e tail +0f output.mdrun_em & -+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_em & ++ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_em & endif -mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em -+g_mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em ++g_mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.g_mdrun_em - echo "mdrun finished" +-echo "mdrun finished" ++echo "g_mdrun finished" echo -n "Press " -@@ -316,9 +316,9 @@ _EOF_ + set ans = $< - echo "Starting grompp..." +@@ -255,7 +255,7 @@ fixed. This is called position restraine + + Position Restrained MD keeps the peptide fixed and lets all water + molecules equilibrate around the peptide in order to fill holes +-etc. which were not filled by the genbox program. ++etc. which were not filled by the g_genbox program. + + We are first going to preprocess the input files to generate the + binary topology. The input files are the topology file, the structure +@@ -274,7 +274,7 @@ performed ( like EM, PR-MD and MD etc. ) + _EOF_ + + if ( $?DISPLAY ) then +- echo "The output of the grompp program should appear" ++ echo "The output of the g_g_grompp program should appear" + echo "in a separate xterm window" + endif + +@@ -318,12 +318,12 @@ gen_seed = 173529 + _EOF_ + + +-echo "Starting grompp..." ++echo "Starting g_grompp..." if ( $?DISPLAY ) then - xterm -title grompp -sb -e tail +0f output.grompp_pr & -+ xterm -title g_grompp -sb -e tail +0f output.grompp_pr & ++ xterm -title g_grompp -sb -e tail +0f output.g_grompp_pr & endif -grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr -+g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr - echo "grompp finished" +-echo "grompp finished" ++g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.g_grompp_pr ++echo "g_grompp finished" + + echo -n "Press " + set ans = $< +@@ -346,19 +346,19 @@ _EOF_ + + if ( $?DISPLAY ) then + echo "Because your DISPLAY variable is set, I will pop up a" +- echo "window with the output of the mdrun program" ++ echo "window with the output of the g_mdrun program" + endif echo -n "Press " -@@ -350,9 +350,9 @@ set ans = $< + set ans = $< - echo "starting mdrun..." +-echo "starting mdrun..." ++echo "starting g_mdrun..." if ( $?DISPLAY ) then - xterm -title mdrun -sb -e tail +0f output.mdrun_pr & -+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_pr & ++ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_pr & endif -mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr -+g_mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr ++g_mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.g_mdrun_pr - echo "mdrun finished" +-echo "mdrun finished" ++echo "g_mdrun finished" echo -n "Press " -@@ -417,9 +417,9 @@ _EOF_ + set ans = $< + +@@ -371,7 +371,7 @@ cat << _EOF_ + ----------------------------------------------------------------- + Now our complete system is finally ready for the actual Molecular + Dynamics simulation. We start again by preprocessing the input files +-by the grompp program to generate the binary topology file (.tpb/.tpr ++by the g_g_grompp program to generate the binary topology file (.tpb/.tpr + extension). + + ----------------------------------------------------------------- +@@ -379,7 +379,7 @@ extension). + _EOF_ - echo "Starting grompp..." + if ( $?DISPLAY ) then +- echo "The output of the grompp program should appear" ++ echo "The output of the g_g_grompp program should appear" + echo "in a separate xterm window" + endif + +@@ -419,13 +419,13 @@ gen_temp = 300.0 + gen_seed = 173529 + _EOF_ + +-echo "Starting grompp..." ++echo "Starting g_grompp..." if ( $?DISPLAY ) then - xterm -title grompp -sb -e tail +0f output.grompp_md & -+ xterm -title g_grompp -sb -e tail +0f output.grompp_md & ++ xterm -title g_grompp -sb -e tail +0f output.g_grompp_md & endif -grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md -+g_grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md ++g_grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.g_grompp_md - echo "grompp finished" +-echo "grompp finished" ++echo "g_grompp finished" echo -n "Press " -@@ -449,9 +449,9 @@ set ans = $< + set ans = $< + +@@ -444,20 +444,20 @@ increasing ( the total number of steps i + _EOF_ + + if ( $?DISPLAY ) then +- echo "The output of the mdrun program should appear" ++ echo "The output of the g_mdrun program should appear" + echo "in a separate xterm window" + endif - echo "starting mdrun..." + echo -n "Press " + set ans = $< + +-echo "starting mdrun..." ++echo "starting g_mdrun..." if ( $?DISPLAY ) then - xterm -title mdrun -sb -e tail +0f output.mdrun_md & -+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_md & ++ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_md & endif -mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md -+g_mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md ++g_mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.g_mdrun_md - echo "mdrun finished" +-echo "mdrun finished" ++echo "g_mdrun finished" echo -n "Press " -@@ -493,7 +493,7 @@ _EOF_ + set ans = $< + +@@ -472,10 +472,10 @@ We are finished simulating, and we are g + trajectory. The trajectory file ( .trj extension ) contains all + coordinates, velocities and forces of all the atoms in our system. + +-The next program we are going run is ngmx. ngmx is a very simple ++The next program we are going run is g_ngmx. g_ngmx is a very simple + trajectory viewer. + +-Once the ngmx program has been started you need to click on a few ++Once the g_ngmx program has been started you need to click on a few + buttons to view your trajectory. + + 1. Once the program has been started a dialog box shows up. Click on +@@ -497,7 +497,7 @@ _EOF_ if ( $?DISPLAY ) then echo Starting Trajectory viewer... diff --git a/gromacs.spec b/gromacs.spec index b9d5a9d..7d16e91 100644 --- a/gromacs.spec +++ b/gromacs.spec @@ -1,6 +1,6 @@ Name: gromacs -Version: 4.5.1 -Release: 2%{?dist} +Version: 4.5.2 +Release: 1%{?dist} Summary: Fast, Free and Flexible Molecular Dynamics Group: Applications/Engineering License: GPLv2+ @@ -19,10 +19,6 @@ Source6: gromacs-README.fedora Patch0: gromacs-GMXRC.patch # Patch gmxdemo for new filenames Patch1: gromacs-gmxdemo.patch -# Patch configure for the library suffix -Patch2: gromacs-configure.patch -# Patch for BZ #644950, CVE-2010-4001 -Patch3: gromacs-4.5.1-gmxrc.patch BuildRequires: cmake BuildRequires: atlas-devel @@ -287,8 +283,6 @@ This package provides tutorials for the use of GROMACS. %setup -q %patch0 -p1 -b .gmxrc %patch1 -p1 -b .gmxdemo -#%patch2 -p1 -b .libsuffix -%patch3 -p1 -b .gmxrc_cve # Fix incorrect permission #chmod a-x src/tools/gmx_xpm2ps.c @@ -490,9 +484,9 @@ mv %{buildroot}%{_bindir}/completion.csh . find %{buildroot} -name *.la -exec rm -rf {} \; # Post install for libs. MPI packages don't need this. -%post -p /sbin/ldconfig +%post libs -p /sbin/ldconfig -%postun -p /sbin/ldconfig +%postun libs -p /sbin/ldconfig %clean rm -rf %{buildroot} @@ -585,6 +579,9 @@ rm -rf %{buildroot} %changelog +* Mon Nov 01 2010 Jussi Lehtola - 4.5.2-1 +- Update to 4.5.2. + * Wed Oct 27 2010 Jussi Lehtola - 4.5.1-2 - Patch around #644950. - Split libraries in own packages to avoid multilib problems. diff --git a/sources b/sources index 5a307c9..64f65d3 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ 0f6d3967f2d8fba5c5668f99dfc6aed7 manual-4.5.pdf -d4b737b0bea8a9390d2c3ad9b159914d gromacs-4.5.1.tar.gz +3d74c7b363a3b124e48424375b49ce67 gromacs-4.5.2.tar.gz