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