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 <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 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 <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_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 <enter>"
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 <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 = $<
@@ -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 <enter>"
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 <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 = $<
@@ -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 <enter>"
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 <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 = $<
@@ -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