diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tutor/gmxdemo/demo

--- gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo	2010-09-29 14:35:03.000000000 +0300

+++ gromacs-4.5.2/share/tutor/gmxdemo/demo	2010-11-01 14:04:34.833273502 +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 <enter>"

 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 <enter>"

 set  ans = $<

@@ -99,14 +99,14 @@ cat << _EOF_

 -----------------------------------------------------------------

 -----------------------------------------------------------------

 Because a simulation of a peptide in vacua 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 boxsize for our system.

 -----------------------------------------------------------------

@@ -114,22 +114,22 @@ right boxsize 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 <enter>"

 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 <enter>"

 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_g_grompp. g_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_g_grompp program should appear"  

         echo "in a separate xterm window"

 endif

@@ -191,13 +191,13 @@ 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 <enter>"

 set  ans = $<

@@ -210,8 +210,8 @@ 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

@@ -224,21 +224,21 @@ 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 <enter>"

 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 <enter>"

 set  ans = $<

@@ -255,7 +255,7 @@ 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. which were not filled by the genbox program.

+etc. which 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

@@ -274,7 +274,7 @@ 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_g_grompp program should appear"  

         echo "in a separate xterm window"

 endif

@@ -318,12 +318,12 @@ 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 <enter>"

 set  ans = $<

@@ -346,19 +346,19 @@ _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 <enter>"

 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 <enter>"

 set  ans = $<

@@ -371,7 +371,7 @@ 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_g_grompp program to generate the binary topology file (.tpb/.tpr

 extension).

 -----------------------------------------------------------------

@@ -379,7 +379,7 @@ extension).

 _EOF_

 if ( $?DISPLAY ) then

-	echo "The output of the grompp program should appear"  

+	echo "The output of the g_g_grompp program should appear"  

         echo "in a separate xterm window"

 endif

@@ -419,13 +419,13 @@ 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 <enter>"

 set  ans = $<

@@ -444,20 +444,20 @@ 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 <enter>"

 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 <enter>"

 set  ans = $<

@@ -472,10 +472,10 @@ We are finished simulating, and we are g

 trajectory. The trajectory file ( .trj 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

@@ -497,7 +497,7 @@ _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