diff -up gromacs-4.5.4/share/tutor/gmxdemo/demo.orig gromacs-4.5.4/share/tutor/gmxdemo/demo --- gromacs-4.5.4/share/tutor/gmxdemo/demo.orig 2011-03-04 13:10:43.000000000 +0200 +++ gromacs-4.5.4/share/tutor/gmxdemo/demo 2011-03-23 15:30:14.004163534 +0200 @@ -58,10 +58,10 @@ cat << _EOF_ ----------------------------------------------------------------- Before we can start any simulation we need a molecular toplogy file. This topology file ( .top extension ) is generated by the -program pdb2gmx. The only input file of the pdb2gmx program is the pdb +program g_pdb2gmx. The only input file of the g_pdb2gmx program is the pdb file of our peptide ( .pdb extension ). -Because most pdb files do not contain all hydrogen atoms, the pdb2gmx +Because most pdb files do not contain all hydrogen atoms, the g_pdb2gmx program will also add them to our peptide. The output file which contains the structure of the peptide when hydrogen atoms are added is a GROMOS structure file ( .gro extension ) @@ -72,22 +72,22 @@ _EOF_ if ( $?DISPLAY ) then echo "You seem to have the DISPLAY variable is set, so we will" - echo "pop up a window with the output of the pdb2gmx program" + echo "pop up a window with the output of the g_pdb2gmx program" endif echo -n "Press " set ans = $< -echo "Starting pdb2gmx" +echo "Starting g_pdb2gmx" if ( $?DISPLAY ) then - xterm -title pdb2gmx -sb -e tail +0f output.pdb2gmx & + xterm -title g_pdb2gmx -sb -e tail +0f output.g_pdb2gmx & endif -pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx << KOKO +g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.g_pdb2gmx << KOKO 1 1 KOKO -echo "pdb2gmx finished" +echo "g_pdb2gmx finished" echo -n "Press " set ans = $< @@ -99,14 +99,14 @@ cat << _EOF_ ----------------------------------------------------------------- ----------------------------------------------------------------- Because a simulation of a peptide in vacuo is a bit unrealistic, we -have to solvate our peptide in a box of water. genbox is the program +have to solvate our peptide in a box of water. g_genbox is the program we use to do this. -The genbox program reads the peptide structure file and an input file -containing the sizes of the desired water box. The output of genbox is +The g_genbox program reads the peptide structure file and an input file +containing the sizes of the desired water box. The output of g_genbox is a GROMOS structure file of a peptide solvated in a box of water. The -genbox program also changes the topology file ( .top extension ) to -include water. First we will use the program editconf to define the +g_genbox program also changes the topology file ( .top extension ) to +include water. First we will use the program g_editconf to define the right box size for our system. ----------------------------------------------------------------- @@ -114,22 +114,22 @@ right box size for our system. _EOF_ if ( $?DISPLAY ) then - echo "The output of the genbox program should appear" + echo "The output of the g_genbox program should appear" echo "in a separate xterm window" endif echo -n "Press " set ans = $< -echo "Starting editconf and genbox..." +echo "Starting g_editconf and g_genbox..." if ( $?DISPLAY ) then - xterm -title genbox -sb -e tail +0f output.genbox & + xterm -title g_genbox -sb -e tail +0f output.g_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.g_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.g_genbox -echo "editconf and genbox finished" +echo "g_editconf and g_genbox finished" echo -n "Press " set ans = $< @@ -142,7 +142,7 @@ cat << _EOF_ ----------------------------------------------------------------- In principle we can start a molecular dynamics simulation now. However it is not very wise to do so, because our system is full of close -contacts. These close contacts are mainly a result of the genbox +contacts. These close contacts are mainly a result of the g_genbox program. The added solvent might have some close contacts with the peptide resulting in very high repulsive energies. If we would start a molecular dynamics (MD) simulation without energy minimisation the @@ -153,7 +153,7 @@ energy minimisation (EM). Energy minimis coordinates of our system to remove high energies from our system. Before we can start the energy minimisation we have to preprocess all -the input files with the GROMACS preprocessor named grompp. grompp +the input files with the GROMACS preprocessor named g_grompp. g_grompp preprocesses the topology file (.top), the structure file (.gro) and a parameter file (.mdp) resulting in a binary topology file (.tpr extension). This binary topology file contains all information for a @@ -163,7 +163,7 @@ simulation (in this case an energy minim _EOF_ if ( $?DISPLAY ) then - echo "The output of the grompp program should appear" + echo "The output of the g_grompp program should appear" echo "in a separate xterm window" endif @@ -190,13 +190,13 @@ emtol = 1000.0 emstep = 0.01 _EOF_ -echo "Starting grompp..." +echo "Starting g_grompp..." if ( $?DISPLAY ) then - xterm -title grompp -sb -e tail +0f output.grompp_em & + xterm -title g_grompp -sb -e tail +0f output.g_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.g_grompp_em -echo "grompp finished" +echo "g_grompp finished" echo -n "Press " set ans = $< @@ -209,8 +209,8 @@ cat << _EOF_ ----------------------------------------------------------------- Now the binary topology file is generated, we can start the energy minimisation (EM). The program which performs the EM is called -mdrun. In fact all simulations are performed by the same program: -mdrun. +g_mdrun. In fact all simulations are performed by the same program: +g_mdrun. As the energy minimisation is running, watch the output of the program. The first number ( from left to right ) is the number of the @@ -223,21 +223,21 @@ rapidly drops down, and converges, to a _EOF_ if ( $?DISPLAY ) then - echo "The output of the mdrun program should appear" + echo "The output of the g_mdrun program should appear" echo "in a separate xterm window" endif echo -n "Press " set ans = $< -echo "starting energy minimisation mdrun..." +echo "starting energy minimisation g_mdrun..." if ( $?DISPLAY ) then - xterm -title mdrun -sb -e tail +0f output.mdrun_em & + xterm -title g_mdrun -sb -e tail +0f output.g_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.g_mdrun_em -echo "mdrun finished" +echo "g_mdrun finished" echo -n "Press " set ans = $< @@ -254,7 +254,7 @@ fixed. This is called position restraine Position restrained MD keeps the peptide fixed and lets all water molecules equilibrate around the peptide in order to fill holes -etc. that were not filled by the genbox program. +etc. that were not filled by the g_genbox program. We are first going to preprocess the input files to generate the binary topology. The input files are the topology file, the structure @@ -273,7 +273,7 @@ performed ( like EM, PR-MD and MD etc. ) _EOF_ if ( $?DISPLAY ) then - echo "The output of the grompp program should appear" + echo "The output of the g_grompp program should appear" echo "in a separate xterm window" endif @@ -317,12 +317,12 @@ gen_seed = 173529 _EOF_ -echo "Starting grompp..." +echo "Starting g_grompp..." if ( $?DISPLAY ) then - xterm -title grompp -sb -e tail +0f output.grompp_pr & + xterm -title g_grompp -sb -e tail +0f output.g_grompp_pr & endif -grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr -echo "grompp finished" +g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.g_grompp_pr +echo "g_grompp finished" echo -n "Press " set ans = $< @@ -345,19 +345,19 @@ _EOF_ if ( $?DISPLAY ) then echo "Because your DISPLAY variable is set, I will pop up a" - echo "window with the output of the mdrun program" + echo "window with the output of the g_mdrun program" endif echo -n "Press " set ans = $< -echo "starting mdrun..." +echo "starting g_mdrun..." if ( $?DISPLAY ) then - xterm -title mdrun -sb -e tail +0f output.mdrun_pr & + xterm -title g_mdrun -sb -e tail +0f output.g_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.g_mdrun_pr -echo "mdrun finished" +echo "g_mdrun finished" echo -n "Press " set ans = $< @@ -370,7 +370,7 @@ cat << _EOF_ ----------------------------------------------------------------- Now our complete system is finally ready for the actual molecular dynamics simulation. We start again by preprocessing the input files -by the grompp program to generate the binary topology file (.tpb/.tpr +by the g_grompp program to generate the binary topology file (.tpb/.tpr extension). ----------------------------------------------------------------- @@ -378,7 +378,7 @@ extension). _EOF_ if ( $?DISPLAY ) then - echo "The output of the grompp program should appear" + echo "The output of the g_grompp program should appear" echo "in a separate xterm window" endif @@ -418,13 +418,13 @@ gen_temp = 300.0 gen_seed = 173529 _EOF_ -echo "Starting grompp..." +echo "Starting g_grompp..." if ( $?DISPLAY ) then - xterm -title grompp -sb -e tail +0f output.grompp_md & + xterm -title g_grompp -sb -e tail +0f output.g_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.g_grompp_md -echo "grompp finished" +echo "g_grompp finished" echo -n "Press " set ans = $< @@ -443,20 +443,20 @@ increasing ( the total number of steps i _EOF_ if ( $?DISPLAY ) then - echo "The output of the mdrun program should appear" + echo "The output of the g_mdrun program should appear" echo "in a separate xterm window" endif echo -n "Press " set ans = $< -echo "starting mdrun..." +echo "starting g_mdrun..." if ( $?DISPLAY ) then - xterm -title mdrun -sb -e tail +0f output.mdrun_md & + xterm -title g_mdrun -sb -e tail +0f output.g_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.g_mdrun_md -echo "mdrun finished" +echo "g_mdrun finished" echo -n "Press " set ans = $< @@ -471,10 +471,10 @@ We are finished simulating, and we are g trajectory. The trajectory file ( .trr extension ) contains all coordinates, velocities and forces of all the atoms in our system. -The next program we are going run is ngmx. ngmx is a very simple +The next program we are going run is g_ngmx. g_ngmx is a very simple trajectory viewer. -Once the ngmx program has been started you need to click on a few +Once the g_ngmx program has been started you need to click on a few buttons to view your trajectory. 1. Once the program has been started a dialog box shows up. Click on @@ -496,7 +496,7 @@ _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