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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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3de3193 |
--- gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo 2010-09-29 14:35:03.000000000 +0300
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3de3193 |
+++ gromacs-4.5.2/share/tutor/gmxdemo/demo 2010-11-01 14:04:34.833273502 +0200
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3de3193 |
@@ -58,10 +58,10 @@ cat << _EOF_
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|
3de3193 |
-----------------------------------------------------------------
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|
|
3de3193 |
Before we can start any simulation we need a molecular toplogy
|
|
|
3de3193 |
file. This topology file ( .top extension ) is generated by the
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|
|
3de3193 |
-program pdb2gmx. The only input file of the pdb2gmx program is the pdb
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|
|
3de3193 |
+program g_pdb2gmx. The only input file of the g_pdb2gmx program is the pdb
|
|
|
3de3193 |
file of our peptide ( .pdb extension ).
|
|
|
2d0f49e |
|
|
|
3de3193 |
-Because most pdb files do not contain all hydrogen atoms, the pdb2gmx
|
|
|
3de3193 |
+Because most pdb files do not contain all hydrogen atoms, the g_pdb2gmx
|
|
|
3de3193 |
program will also add them to our peptide. The output file which
|
|
|
3de3193 |
contains the structure of the peptide when hydrogen atoms are added is a
|
|
|
3de3193 |
gromos structure file ( .gro extension )
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|
|
3de3193 |
@@ -72,22 +72,22 @@ _EOF_
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3de3193 |
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|
3de3193 |
if ( $?DISPLAY ) then
|
|
|
3de3193 |
echo "You seem to have the DISPLAY variable is set, so we will"
|
|
|
3de3193 |
- echo "pop up a window with the output of the pdb2gmx program"
|
|
|
3de3193 |
+ echo "pop up a window with the output of the g_pdb2gmx program"
|
|
|
3de3193 |
endif
|
|
|
3de3193 |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
3de3193 |
|
|
|
3de3193 |
|
|
|
3de3193 |
-echo "Starting pdb2gmx"
|
|
|
3de3193 |
+echo "Starting g_pdb2gmx"
|
|
|
2d0f49e |
if ( $?DISPLAY ) then
|
|
|
2d0f49e |
- xterm -title pdb2gmx -sb -e tail +0f output.pdb2gmx &
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|
3de3193 |
+ xterm -title g_pdb2gmx -sb -e tail +0f output.g_pdb2gmx &
|
|
|
3de3193 |
endif
|
|
|
3de3193 |
-pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx << KOKO
|
|
|
3de3193 |
+g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.g_pdb2gmx << KOKO
|
|
|
3de3193 |
1
|
|
|
3de3193 |
1
|
|
|
3de3193 |
KOKO
|
|
|
3de3193 |
|
|
|
3de3193 |
-echo "pdb2gmx finished"
|
|
|
3de3193 |
+echo "g_pdb2gmx finished"
|
|
|
3de3193 |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
3de3193 |
|
|
|
3de3193 |
@@ -99,14 +99,14 @@ cat << _EOF_
|
|
|
3de3193 |
-----------------------------------------------------------------
|
|
|
3de3193 |
-----------------------------------------------------------------
|
|
|
3de3193 |
Because a simulation of a peptide in vacua is a bit unrealistic, we
|
|
|
3de3193 |
-have to solvate our peptide in a box of water. genbox is the program
|
|
|
3de3193 |
+have to solvate our peptide in a box of water. g_genbox is the program
|
|
|
3de3193 |
we use to do this.
|
|
|
3de3193 |
|
|
|
3de3193 |
-The genbox program reads the peptide structure file and an input file
|
|
|
3de3193 |
-containing the sizes of the desired water box. The output of genbox is
|
|
|
3de3193 |
+The g_genbox program reads the peptide structure file and an input file
|
|
|
3de3193 |
+containing the sizes of the desired water box. The output of g_genbox is
|
|
|
3de3193 |
a gromos structure file of a peptide solvated in a box of water. The
|
|
|
3de3193 |
-genbox program also changes the topology file ( .top extension ) to
|
|
|
3de3193 |
-include water. First we will use the program editconf to define the
|
|
|
3de3193 |
+g_genbox program also changes the topology file ( .top extension ) to
|
|
|
3de3193 |
+include water. First we will use the program g_editconf to define the
|
|
|
3de3193 |
right boxsize for our system.
|
|
|
3de3193 |
|
|
|
3de3193 |
-----------------------------------------------------------------
|
|
|
3de3193 |
@@ -114,22 +114,22 @@ right boxsize for our system.
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
if ( $?DISPLAY ) then
|
|
|
3de3193 |
- echo "The output of the genbox program should appear"
|
|
|
3de3193 |
+ echo "The output of the g_genbox program should appear"
|
|
|
3de3193 |
echo "in a separate xterm window"
|
|
|
2d0f49e |
endif
|
|
|
3de3193 |
|
|
|
2d0f49e |
echo -n "Press <enter>"
|
|
|
2d0f49e |
set ans = $<
|
|
|
2d0f49e |
|
|
|
3de3193 |
-echo "Starting editconf and genbox..."
|
|
|
3de3193 |
+echo "Starting g_editconf and g_genbox..."
|
|
|
2d0f49e |
if ( $?DISPLAY ) then
|
|
|
2d0f49e |
- xterm -title genbox -sb -e tail +0f output.genbox &
|
|
|
3de3193 |
+ xterm -title g_genbox -sb -e tail +0f output.g_genbox &
|
|
|
2d0f49e |
endif
|
|
|
2d0f49e |
-editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.genbox
|
|
|
3de3193 |
+g_editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.g_genbox
|
|
|
2d0f49e |
|
|
|
2d0f49e |
-genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.genbox
|
|
|
3de3193 |
+g_genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.g_genbox
|
|
|
2d0f49e |
|
|
|
3de3193 |
-echo "editconf and genbox finished"
|
|
|
3de3193 |
+echo "g_editconf and g_genbox finished"
|
|
|
2d0f49e |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
2d0f49e |
|
|
|
3de3193 |
@@ -142,7 +142,7 @@ cat << _EOF_
|
|
|
3de3193 |
-----------------------------------------------------------------
|
|
|
3de3193 |
In principle we can start a Molecular Dynamics simulation now. However
|
|
|
3de3193 |
it is not very wise to do so, because our system is full of close
|
|
|
3de3193 |
-contacts. These close contacts are mainly a result of the genbox
|
|
|
3de3193 |
+contacts. These close contacts are mainly a result of the g_genbox
|
|
|
3de3193 |
program. The added solvent might have some close contacts with the
|
|
|
3de3193 |
peptide resulting in very high repulsive energies. If we would start a
|
|
|
3de3193 |
Molecular Dynamics (MD) simulation without energy minimisation the
|
|
|
3de3193 |
@@ -153,7 +153,7 @@ Energy Minimisation (EM). Energy minimis
|
|
|
3de3193 |
coordinates of our system to remove high energies from our system.
|
|
|
3de3193 |
|
|
|
3de3193 |
Before we can start the Energy Minimisation we have to preprocess all
|
|
|
3de3193 |
-the input files with the GROMACS preprocessor named grompp. grompp
|
|
|
3de3193 |
+the input files with the GROMACS preprocessor named g_g_grompp. g_g_grompp
|
|
|
3de3193 |
preprocesses the topology file (.top), the structure file (.gro) and a
|
|
|
3de3193 |
parameter file (.mdp) resulting in a binary topology file (.tpr
|
|
|
3de3193 |
extension). This binary topology file contains all information for a
|
|
|
3de3193 |
@@ -163,7 +163,7 @@ simulation (in this case an energy minim
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
if ( $?DISPLAY ) then
|
|
|
3de3193 |
- echo "The output of the grompp program should appear"
|
|
|
3de3193 |
+ echo "The output of the g_g_grompp program should appear"
|
|
|
3de3193 |
echo "in a separate xterm window"
|
|
|
3de3193 |
endif
|
|
|
3de3193 |
|
|
|
3de3193 |
@@ -191,13 +191,13 @@ emtol = 1000.0
|
|
|
3de3193 |
emstep = 0.01
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
-echo "Starting grompp..."
|
|
|
3de3193 |
+echo "Starting g_grompp..."
|
|
|
2d0f49e |
if ( $?DISPLAY ) then
|
|
|
2d0f49e |
- xterm -title grompp -sb -e tail +0f output.grompp_em &
|
|
|
3de3193 |
+ xterm -title g_grompp -sb -e tail +0f output.g_grompp_em &
|
|
|
2d0f49e |
endif
|
|
|
2d0f49e |
-grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em
|
|
|
3de3193 |
+g_grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.g_grompp_em
|
|
|
2d0f49e |
|
|
|
3de3193 |
-echo "grompp finished"
|
|
|
3de3193 |
+echo "g_grompp finished"
|
|
|
2d0f49e |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
3de3193 |
|
|
|
3de3193 |
@@ -210,8 +210,8 @@ cat << _EOF_
|
|
|
3de3193 |
-----------------------------------------------------------------
|
|
|
3de3193 |
Now the binary topology file is generated, we can start the energy
|
|
|
3de3193 |
minimisation (EM). The program which performs the EM is called
|
|
|
3de3193 |
-mdrun. In fact all simulations are performed by the same program:
|
|
|
3de3193 |
-mdrun.
|
|
|
3de3193 |
+g_mdrun. In fact all simulations are performed by the same program:
|
|
|
3de3193 |
+g_mdrun.
|
|
|
3de3193 |
|
|
|
3de3193 |
As the Energy Minimisation is running, watch the output of the
|
|
|
3de3193 |
program. The first number ( from left to right ) is the number of the
|
|
|
3de3193 |
@@ -224,21 +224,21 @@ rapidly drops down, and converges, to a
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
if ( $?DISPLAY ) then
|
|
|
3de3193 |
- echo "The output of the mdrun program should appear"
|
|
|
3de3193 |
+ echo "The output of the g_mdrun program should appear"
|
|
|
3de3193 |
echo "in a separate xterm window"
|
|
|
3de3193 |
endif
|
|
|
3de3193 |
|
|
|
3de3193 |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
3de3193 |
|
|
|
3de3193 |
-echo "starting energy minimisation mdrun..."
|
|
|
3de3193 |
+echo "starting energy minimisation g_mdrun..."
|
|
|
2d0f49e |
|
|
|
2d0f49e |
if ( $?DISPLAY ) then
|
|
|
2d0f49e |
- xterm -title mdrun -sb -e tail +0f output.mdrun_em &
|
|
|
3de3193 |
+ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_em &
|
|
|
2d0f49e |
endif
|
|
|
2d0f49e |
-mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em
|
|
|
3de3193 |
+g_mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.g_mdrun_em
|
|
|
2d0f49e |
|
|
|
3de3193 |
-echo "mdrun finished"
|
|
|
3de3193 |
+echo "g_mdrun finished"
|
|
|
2d0f49e |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
2d0f49e |
|
|
|
3de3193 |
@@ -255,7 +255,7 @@ fixed. This is called position restraine
|
|
|
3de3193 |
|
|
|
3de3193 |
Position Restrained MD keeps the peptide fixed and lets all water
|
|
|
3de3193 |
molecules equilibrate around the peptide in order to fill holes
|
|
|
3de3193 |
-etc. which were not filled by the genbox program.
|
|
|
3de3193 |
+etc. which were not filled by the g_genbox program.
|
|
|
3de3193 |
|
|
|
3de3193 |
We are first going to preprocess the input files to generate the
|
|
|
3de3193 |
binary topology. The input files are the topology file, the structure
|
|
|
3de3193 |
@@ -274,7 +274,7 @@ performed ( like EM, PR-MD and MD etc. )
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
if ( $?DISPLAY ) then
|
|
|
3de3193 |
- echo "The output of the grompp program should appear"
|
|
|
3de3193 |
+ echo "The output of the g_g_grompp program should appear"
|
|
|
3de3193 |
echo "in a separate xterm window"
|
|
|
3de3193 |
endif
|
|
|
3de3193 |
|
|
|
3de3193 |
@@ -318,12 +318,12 @@ gen_seed = 173529
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
|
|
|
3de3193 |
-echo "Starting grompp..."
|
|
|
3de3193 |
+echo "Starting g_grompp..."
|
|
|
2d0f49e |
if ( $?DISPLAY ) then
|
|
|
2d0f49e |
- xterm -title grompp -sb -e tail +0f output.grompp_pr &
|
|
|
3de3193 |
+ xterm -title g_grompp -sb -e tail +0f output.g_grompp_pr &
|
|
|
2d0f49e |
endif
|
|
|
2d0f49e |
-grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr
|
|
|
3de3193 |
-echo "grompp finished"
|
|
|
3de3193 |
+g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.g_grompp_pr
|
|
|
3de3193 |
+echo "g_grompp finished"
|
|
|
3de3193 |
|
|
|
3de3193 |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
3de3193 |
@@ -346,19 +346,19 @@ _EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
if ( $?DISPLAY ) then
|
|
|
3de3193 |
echo "Because your DISPLAY variable is set, I will pop up a"
|
|
|
3de3193 |
- echo "window with the output of the mdrun program"
|
|
|
3de3193 |
+ echo "window with the output of the g_mdrun program"
|
|
|
3de3193 |
endif
|
|
|
2d0f49e |
|
|
|
2d0f49e |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
2d0f49e |
|
|
|
3de3193 |
-echo "starting mdrun..."
|
|
|
3de3193 |
+echo "starting g_mdrun..."
|
|
|
2d0f49e |
if ( $?DISPLAY ) then
|
|
|
2d0f49e |
- xterm -title mdrun -sb -e tail +0f output.mdrun_pr &
|
|
|
3de3193 |
+ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_pr &
|
|
|
2d0f49e |
endif
|
|
|
2d0f49e |
-mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr
|
|
|
3de3193 |
+g_mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.g_mdrun_pr
|
|
|
2d0f49e |
|
|
|
3de3193 |
-echo "mdrun finished"
|
|
|
3de3193 |
+echo "g_mdrun finished"
|
|
|
2d0f49e |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
3de3193 |
|
|
|
3de3193 |
@@ -371,7 +371,7 @@ cat << _EOF_
|
|
|
3de3193 |
-----------------------------------------------------------------
|
|
|
3de3193 |
Now our complete system is finally ready for the actual Molecular
|
|
|
3de3193 |
Dynamics simulation. We start again by preprocessing the input files
|
|
|
3de3193 |
-by the grompp program to generate the binary topology file (.tpb/.tpr
|
|
|
3de3193 |
+by the g_g_grompp program to generate the binary topology file (.tpb/.tpr
|
|
|
3de3193 |
extension).
|
|
|
3de3193 |
|
|
|
3de3193 |
-----------------------------------------------------------------
|
|
|
3de3193 |
@@ -379,7 +379,7 @@ extension).
|
|
|
3de3193 |
_EOF_
|
|
|
2d0f49e |
|
|
|
3de3193 |
if ( $?DISPLAY ) then
|
|
|
3de3193 |
- echo "The output of the grompp program should appear"
|
|
|
3de3193 |
+ echo "The output of the g_g_grompp program should appear"
|
|
|
3de3193 |
echo "in a separate xterm window"
|
|
|
3de3193 |
endif
|
|
|
3de3193 |
|
|
|
3de3193 |
@@ -419,13 +419,13 @@ gen_temp = 300.0
|
|
|
3de3193 |
gen_seed = 173529
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
-echo "Starting grompp..."
|
|
|
3de3193 |
+echo "Starting g_grompp..."
|
|
|
2d0f49e |
if ( $?DISPLAY ) then
|
|
|
2d0f49e |
- xterm -title grompp -sb -e tail +0f output.grompp_md &
|
|
|
3de3193 |
+ xterm -title g_grompp -sb -e tail +0f output.g_grompp_md &
|
|
|
2d0f49e |
endif
|
|
|
2d0f49e |
-grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md
|
|
|
3de3193 |
+g_grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.g_grompp_md
|
|
|
2d0f49e |
|
|
|
3de3193 |
-echo "grompp finished"
|
|
|
3de3193 |
+echo "g_grompp finished"
|
|
|
2d0f49e |
echo -n "Press <enter>"
|
|
|
3de3193 |
set ans = $<
|
|
|
3de3193 |
|
|
|
3de3193 |
@@ -444,20 +444,20 @@ increasing ( the total number of steps i
|
|
|
3de3193 |
_EOF_
|
|
|
3de3193 |
|
|
|
3de3193 |
if ( $?DISPLAY ) then
|
|
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3de3193 |
- 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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2d0f49e |
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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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2d0f49e |
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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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2d0f49e |
+ g_ngmx -f ${MOL}_md -s ${MOL}_md &
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2d0f49e |
endif
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2d0f49e |
#last line
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