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diff -up gromacs-4.0.3/share/tutor/gmxdemo/demo.orig gromacs-4.0.3/share/tutor/gmxdemo/demo
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--- gromacs-4.0.3/share/tutor/gmxdemo/demo.orig 2006-02-15 23:48:34.000000000 +0200
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+++ gromacs-4.0.3/share/tutor/gmxdemo/demo 2009-01-19 16:52:35.000000000 +0200
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@@ -80,9 +80,9 @@ set ans = $<
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echo "Starting pdb2gmx"
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if ( $?DISPLAY ) then
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- xterm -title pdb2gmx -sb -e tail +0f output.pdb2gmx &
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+ xterm -title g_pdb2gmx -sb -e tail +0f output.pdb2gmx &
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endif
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-echo 0 | pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx
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+echo 0 | g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx
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echo "pdb2gmx finished"
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echo -n "Press <enter>"
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set ans = $<
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@@ -119,11 +119,11 @@ set ans = $<
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echo "Starting editconf and genbox..."
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if ( $?DISPLAY ) then
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- xterm -title genbox -sb -e tail +0f output.genbox &
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+ xterm -title g_genbox -sb -e tail +0f output.genbox &
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endif
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-editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.genbox
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+g_editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.genbox
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-genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.genbox
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+g_genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.genbox
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echo "editconf and genbox finished"
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echo -n "Press <enter>"
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@@ -189,9 +189,9 @@ _EOF_
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echo "Starting grompp..."
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if ( $?DISPLAY ) then
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- xterm -title grompp -sb -e tail +0f output.grompp_em &
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+ xterm -title g_grompp -sb -e tail +0f output.grompp_em &
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endif
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-grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em
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+g_grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em
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echo "grompp finished"
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echo -n "Press <enter>"
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@@ -230,9 +230,9 @@ set ans = $<
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echo "starting energy minimisation mdrun..."
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if ( $?DISPLAY ) then
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- xterm -title mdrun -sb -e tail +0f output.mdrun_em &
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+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_em &
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endif
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-mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em
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+g_mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em
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echo "mdrun finished"
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echo -n "Press <enter>"
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@@ -316,9 +316,9 @@ _EOF_
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echo "Starting grompp..."
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if ( $?DISPLAY ) then
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- xterm -title grompp -sb -e tail +0f output.grompp_pr &
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+ xterm -title g_grompp -sb -e tail +0f output.grompp_pr &
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endif
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-grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr
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+g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr
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echo "grompp finished"
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echo -n "Press <enter>"
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@@ -350,9 +350,9 @@ set ans = $<
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echo "starting mdrun..."
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if ( $?DISPLAY ) then
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- xterm -title mdrun -sb -e tail +0f output.mdrun_pr &
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+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_pr &
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endif
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-mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr
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+g_mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr
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echo "mdrun finished"
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echo -n "Press <enter>"
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@@ -417,9 +417,9 @@ _EOF_
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echo "Starting grompp..."
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if ( $?DISPLAY ) then
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- xterm -title grompp -sb -e tail +0f output.grompp_md &
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+ xterm -title g_grompp -sb -e tail +0f output.grompp_md &
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endif
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-grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md
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+g_grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md
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echo "grompp finished"
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echo -n "Press <enter>"
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@@ -449,9 +449,9 @@ set ans = $<
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echo "starting mdrun..."
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if ( $?DISPLAY ) then
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- xterm -title mdrun -sb -e tail +0f output.mdrun_md &
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+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_md &
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endif
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-mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md
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+g_mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md
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echo "mdrun finished"
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echo -n "Press <enter>"
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@@ -493,7 +493,7 @@ _EOF_
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if ( $?DISPLAY ) then
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echo Starting Trajectory viewer...
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- ngmx -f ${MOL}_md -s ${MOL}_md &
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+ g_ngmx -f ${MOL}_md -s ${MOL}_md &
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endif
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#last line
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