diff --git a/gromacs-gmxdemo.patch b/gromacs-gmxdemo.patch new file mode 100644 index 0000000..7160fb2 --- /dev/null +++ b/gromacs-gmxdemo.patch @@ -0,0 +1,111 @@ +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 = $< + + echo "Starting pdb2gmx" + if ( $?DISPLAY ) then +- xterm -title pdb2gmx -sb -e tail +0f output.pdb2gmx & ++ xterm -title g_pdb2gmx -sb -e tail +0f output.pdb2gmx & + 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..." + if ( $?DISPLAY ) then +- xterm -title genbox -sb -e tail +0f output.genbox & ++ xterm -title g_genbox -sb -e tail +0f output.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 + +-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 + + echo "editconf and genbox finished" + echo -n "Press " +@@ -189,9 +189,9 @@ _EOF_ + + echo "Starting 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 & + 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 + + echo "grompp finished" + echo -n "Press " +@@ -230,9 +230,9 @@ set ans = $< + echo "starting energy minimisation 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 & + 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 + + echo "mdrun finished" + echo -n "Press " +@@ -316,9 +316,9 @@ _EOF_ + + echo "Starting 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 & + 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 -n "Press " +@@ -350,9 +350,9 @@ set ans = $< + + echo "starting 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 & + 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 + + echo "mdrun finished" + echo -n "Press " +@@ -417,9 +417,9 @@ _EOF_ + + echo "Starting 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 & + 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 + + echo "grompp finished" + echo -n "Press " +@@ -449,9 +449,9 @@ set ans = $< + + echo "starting 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 & + 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 + + echo "mdrun finished" + echo -n "Press " +@@ -493,7 +493,7 @@ _EOF_ + + if ( $?DISPLAY ) then + echo Starting Trajectory viewer... +- ngmx -f ${MOL}_md -s ${MOL}_md & ++ g_ngmx -f ${MOL}_md -s ${MOL}_md & + endif + #last line + diff --git a/gromacs.spec b/gromacs.spec index dc7c19f..0c8027a 100644 --- a/gromacs.spec +++ b/gromacs.spec @@ -1,7 +1,7 @@ Name: gromacs Version: 4.0.3 -Release: 2%{?dist} -Summary: GROMACS binaries +Release: 3%{?dist} +Summary: GROMACS - Fast, Free and Flexible Molecular Dynamics Group: Applications/Engineering License: GPLv2+ URL: http://www.gromacs.org @@ -15,6 +15,8 @@ Source6: gromacs-README.fedora # Add shebangs to scripts Patch0: gromacs-GMXRC.patch +# Patch gmxdemo for new filenames +Patch1: gromacs-gmxdemo.patch BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) Requires: gromacs-common = %{version}-%{release} @@ -260,6 +262,7 @@ This package provides tutorials for the use of GROMACS. %prep %setup -q %patch0 -p1 +%patch1 -p1 # Fix incorrect permission chmod a-x src/tools/gmx_xpm2ps.c @@ -546,6 +549,9 @@ rm -rf %{buildroot} %changelog +* Mon Jan 19 2009 Jussi Lehtola - 4.0.3-3 +- Fixed gmxdemo. + * Mon Jan 19 2009 Jussi Lehtola - 4.0.3-2 - Fix EPEL 4 build.