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