rpms/gromacs/devel gromacs-gmxdemo.patch, NONE, 1.1 gromacs.spec, 1.7, 1.8 import.log, 1.6, 1.7
Jussi Lehtola
jussilehtola at fedoraproject.org
Mon Jan 19 14:55:51 UTC 2009
Author: jussilehtola
Update of /cvs/pkgs/rpms/gromacs/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv19049/devel
Modified Files:
gromacs.spec import.log
Added Files:
gromacs-gmxdemo.patch
Log Message:
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola at iki.fi> - 4.0.3-3
- Fixed gmxdemo.
gromacs-gmxdemo.patch:
--- NEW FILE gromacs-gmxdemo.patch ---
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 <enter>"
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 <enter>"
@@ -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 <enter>"
@@ -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 <enter>"
@@ -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 <enter>"
@@ -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 <enter>"
@@ -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 <enter>"
@@ -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 <enter>"
@@ -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
Index: gromacs.spec
===================================================================
RCS file: /cvs/pkgs/rpms/gromacs/devel/gromacs.spec,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- gromacs.spec 19 Jan 2009 12:18:05 -0000 1.7
+++ gromacs.spec 19 Jan 2009 14:55:21 -0000 1.8
@@ -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 @@
# 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 @@
%prep
%setup -q
%patch0 -p1
+%patch1 -p1
# Fix incorrect permission
chmod a-x src/tools/gmx_xpm2ps.c
@@ -546,6 +549,9 @@
%changelog
+* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola at iki.fi> - 4.0.3-3
+- Fixed gmxdemo.
+
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola at iki.fi> - 4.0.3-2
- Fix EPEL 4 build.
Index: import.log
===================================================================
RCS file: /cvs/pkgs/rpms/gromacs/devel/import.log,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- import.log 19 Jan 2009 12:18:05 -0000 1.6
+++ import.log 19 Jan 2009 14:55:21 -0000 1.7
@@ -4,3 +4,4 @@
gromacs-4_0_2-7_fc10:HEAD:gromacs-4.0.2-7.fc10.src.rpm:1231935162
gromacs-4_0_3-1_fc10:HEAD:gromacs-4.0.3-1.fc10.src.rpm:1232356764
gromacs-4_0_3-2_fc10:HEAD:gromacs-4.0.3-2.fc10.src.rpm:1232367441
+gromacs-4_0_3-3_fc10:HEAD:gromacs-4.0.3-3.fc10.src.rpm:1232376891
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