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diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tutor/gmxdemo/demo
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--- gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo	2010-09-29 14:35:03.000000000 +0300
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+++ gromacs-4.5.2/share/tutor/gmxdemo/demo	2010-11-01 14:04:34.833273502 +0200
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@@ -58,10 +58,10 @@ cat << _EOF_
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 -----------------------------------------------------------------
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 Before we can start any simulation we need a molecular toplogy
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 file. This topology file ( .top extension ) is generated by the
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-program pdb2gmx. The only input file of the pdb2gmx program is the pdb
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+program g_pdb2gmx. The only input file of the g_pdb2gmx program is the pdb
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 file of our peptide ( .pdb extension ). 
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-Because most pdb files do not contain all hydrogen atoms, the pdb2gmx
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+Because most pdb files do not contain all hydrogen atoms, the g_pdb2gmx
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 program will also add them to our peptide. The output file which
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 contains the structure of the peptide when hydrogen atoms are added is a
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 gromos structure file ( .gro extension )  
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@@ -72,22 +72,22 @@ _EOF_
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 if ( $?DISPLAY ) then
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 	echo "You seem to have the DISPLAY variable is set, so we will"
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-        echo "pop up a window with the output of the pdb2gmx program"  
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+        echo "pop up a window with the output of the g_pdb2gmx program"  
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 endif
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 echo -n "Press <enter>"
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 set  ans = $<
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-echo "Starting pdb2gmx"
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+echo "Starting g_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.g_pdb2gmx &
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 endif
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-pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx << KOKO
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+g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.g_pdb2gmx << KOKO
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 1
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 1
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 KOKO
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-echo "pdb2gmx finished"
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+echo "g_pdb2gmx finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -99,14 +99,14 @@ cat << _EOF_
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 -----------------------------------------------------------------
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 -----------------------------------------------------------------
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 Because a simulation of a peptide in vacua is a bit unrealistic, we
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-have to solvate our peptide in a box of water. genbox is the program
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+have to solvate our peptide in a box of water. g_genbox is the program
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 we use to do this.
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-The genbox program reads the peptide structure file and an input file
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-containing the sizes of the desired water box. The output of genbox is
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+The g_genbox program reads the peptide structure file and an input file
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+containing the sizes of the desired water box. The output of g_genbox is
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 a gromos structure file of a peptide solvated in a box of water. The
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-genbox program also changes the topology file ( .top extension ) to
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-include water. First we will use the program editconf to define the
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+g_genbox program also changes the topology file ( .top extension ) to
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+include water. First we will use the program g_editconf to define the
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 right boxsize for our system.
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 -----------------------------------------------------------------
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@@ -114,22 +114,22 @@ right boxsize for our system.
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 _EOF_
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 if ( $?DISPLAY ) then
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-	echo "The output of the genbox program should appear"
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+	echo "The output of the g_genbox program should appear"
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         echo "in a separate xterm window"  
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 endif
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 echo -n "Press <enter>"
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 set  ans = $<
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-echo "Starting editconf and genbox..."
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+echo "Starting g_editconf and g_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.g_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.g_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.g_genbox 
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-echo "editconf and genbox finished"
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+echo "g_editconf and g_genbox finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -142,7 +142,7 @@ cat << _EOF_
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 -----------------------------------------------------------------
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 In principle we can start a Molecular Dynamics simulation now. However
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 it is not very wise to do so, because our system is full of close
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-contacts. These close contacts are mainly a result of the genbox
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+contacts. These close contacts are mainly a result of the g_genbox
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 program. The added solvent might have some close contacts with the
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 peptide resulting in very high repulsive energies. If we would start a
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 Molecular Dynamics (MD) simulation without energy minimisation the
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@@ -153,7 +153,7 @@ Energy Minimisation (EM). Energy minimis
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 coordinates of our system to remove high energies from our system.  
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 Before we can start the Energy Minimisation we have to preprocess all
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-the input files with the GROMACS preprocessor named grompp. grompp
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+the input files with the GROMACS preprocessor named g_g_grompp. g_g_grompp
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 preprocesses the topology file (.top), the structure file (.gro) and a
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 parameter file (.mdp) resulting in a binary topology file (.tpr
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 extension). This binary topology file contains all information for a 
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@@ -163,7 +163,7 @@ simulation (in this case an energy minim
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 _EOF_
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 if ( $?DISPLAY ) then
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-	echo "The output of the grompp program should appear"  
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+	echo "The output of the g_g_grompp program should appear"  
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         echo "in a separate xterm window"
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 endif
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@@ -191,13 +191,13 @@ emtol               =  1000.0
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 emstep              =  0.01
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 _EOF_
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-echo "Starting grompp..."
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+echo "Starting g_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.g_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.g_grompp_em
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-echo "grompp finished"
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+echo "g_grompp finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -210,8 +210,8 @@ cat << _EOF_
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 -----------------------------------------------------------------
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 Now the binary topology file is generated, we can start the energy
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 minimisation (EM). The program which performs the EM is called
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-mdrun. In fact all simulations are performed by the same program:
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-mdrun. 
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+g_mdrun. In fact all simulations are performed by the same program:
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+g_mdrun. 
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 As the Energy Minimisation is running, watch the output of the
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 program. The first number ( from left to right ) is the number of the
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@@ -224,21 +224,21 @@ rapidly drops down, and converges, to a 
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 _EOF_
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 if ( $?DISPLAY ) then
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-	echo "The output of the mdrun program should appear"
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+	echo "The output of the g_mdrun program should appear"
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         echo "in a separate xterm window"
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 endif
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 echo -n "Press <enter>"
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 set  ans = $<
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-echo "starting energy minimisation mdrun..."
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+echo "starting energy minimisation g_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.g_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.g_mdrun_em 
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-echo "mdrun finished"
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+echo "g_mdrun finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -255,7 +255,7 @@ fixed. This is called position restraine
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 Position Restrained MD keeps the peptide fixed and lets all water
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 molecules equilibrate around the peptide in order to fill holes
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-etc. which were not filled by the genbox program.
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+etc. which were not filled by the g_genbox program.
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 We are first going to preprocess the input files to generate the
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 binary topology. The input files are the topology file, the structure
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@@ -274,7 +274,7 @@ performed ( like EM, PR-MD and MD etc. )
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 _EOF_
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 if ( $?DISPLAY ) then
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-	echo "The output of the grompp program should appear"  
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+	echo "The output of the g_g_grompp program should appear"  
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         echo "in a separate xterm window"
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 endif
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@@ -318,12 +318,12 @@ gen_seed            =  173529
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 _EOF_
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-echo "Starting grompp..."
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+echo "Starting g_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.g_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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-echo "grompp finished"
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+g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.g_grompp_pr
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+echo "g_grompp finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -346,19 +346,19 @@ _EOF_
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 if ( $?DISPLAY ) then
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 	echo "Because your DISPLAY variable is set, I will pop up a" 
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-	echo "window with the output of the mdrun program"  
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+	echo "window with the output of the g_mdrun program"  
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 endif
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 echo -n "Press <enter>"
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 set  ans = $<
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-echo "starting mdrun..."
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+echo "starting g_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.g_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.g_mdrun_pr
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-echo "mdrun finished"
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+echo "g_mdrun finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -371,7 +371,7 @@ cat << _EOF_
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 -----------------------------------------------------------------
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 Now our complete system is finally ready for the actual Molecular
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 Dynamics simulation. We start again by preprocessing the input files
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-by the grompp program to generate the binary topology file (.tpb/.tpr
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+by the g_g_grompp program to generate the binary topology file (.tpb/.tpr
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 extension).
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 -----------------------------------------------------------------
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@@ -379,7 +379,7 @@ extension).
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 _EOF_
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 if ( $?DISPLAY ) then
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-	echo "The output of the grompp program should appear"  
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+	echo "The output of the g_g_grompp program should appear"  
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         echo "in a separate xterm window"
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 endif
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@@ -419,13 +419,13 @@ gen_temp            =  300.0
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 gen_seed            =  173529
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 _EOF_
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-echo "Starting grompp..."
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+echo "Starting g_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.g_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.g_grompp_md
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-echo "grompp finished"
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+echo "g_grompp finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -444,20 +444,20 @@ increasing ( the total number of steps i
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 _EOF_
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 if ( $?DISPLAY ) then
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-	echo "The output of the mdrun program should appear"  
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+	echo "The output of the g_mdrun program should appear"  
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         echo "in a separate xterm window"
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 endif
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 echo -n "Press <enter>"
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 set  ans = $<
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-echo "starting mdrun..."
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+echo "starting g_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.g_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.g_mdrun_md
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-echo "mdrun finished"
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+echo "g_mdrun finished"
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 echo -n "Press <enter>"
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 set  ans = $<
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@@ -472,10 +472,10 @@ We are finished simulating, and we are g
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 trajectory. The trajectory file ( .trj extension ) contains all
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 coordinates, velocities and forces of all the atoms in our system. 
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-The next program we are going run is ngmx. ngmx is a very simple
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+The next program we are going run is g_ngmx. g_ngmx is a very simple
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 trajectory viewer. 
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-Once the ngmx program has been started you need to click on a few
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+Once the g_ngmx program has been started you need to click on a few
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 buttons to view your trajectory.
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 1. Once the program has been started a dialog box shows up. Click on
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@@ -497,7 +497,7 @@ _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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