demo

最著名最快的分子模拟软件

use two of those groups: Protein and SOL(vent). We use these groups to
put position restraints on all the atoms of the peptide.

The parameter file ( .mdp extension ) contains all information about
the PR-MD like: step size, number of steps, temperature, etc. This
Paramter file also tells GROMACS what kind of simulation should be
performed ( like EM, PR-MD and MD etc. )
-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_

if ( $?DISPLAY ) then
	echo "The output of the grompp program should appear"  
        echo "in a separate xterm window"
endif

echo -n "Press <enter>"
set  ans = $<

echo "generating parameter file..."
cat > pr.mdp << _EOF_
title               =  ${MOL} position restraining
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  500	; total 1.0 ps.
nstcomm             =  1
nstxout             =  10
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1      	0.1
tc-grps		    =  protein  	sol
ref_t               =  300      	300
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
_EOF_


echo "Starting grompp..."
if ( $?DISPLAY ) then 
	xterm -title grompp -sb -e tail +0f output.grompp_pr &
endif
grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr
echo "grompp finished"

echo -n "Press <enter>"
set  ans = $<

################
### MDRUN PR ###
################
clear
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
Now we start the Position restrained Molecular Dynamics simulation. It
is important to note that in this example the simulated time is too
short (1 ps) to equilibrate our system completely, but that would simple take
too much time. ( about one day ). 

-----------------------------------------------------------------
-----------------------------------------------------------------
_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"  
endif

echo -n "Press <enter>"
set  ans = $<

echo "starting mdrun..."
if ( $?DISPLAY ) then 
	xterm -title mdrun -sb -e tail +0f output.mdrun_pr &
endif
mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr

echo "mdrun finished"
echo -n "Press <enter>"
set  ans = $<

#################
### GROMPP MD ###
#################
clear
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
extension).

-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_

if ( $?DISPLAY ) then
	echo "The output of the grompp program should appear"  
        echo "in a separate xterm window"
endif

echo -n "Press <enter>"
set  ans = $<

echo "generating parameter file..."
cat > md.mdp << _EOF_
title               =  ${MOL} MD
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  5000	; total 5 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1	     0.1
tc-grps		    =  protein	     sol
ref_t               =  300	     300
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
_EOF_

echo "Starting grompp..."
if ( $?DISPLAY ) then 
	xterm -title grompp -sb -e tail +0f output.grompp_md &
endif
grompp -f md -c ${MOL}_b4md  -p ${MOL} -o ${MOL}_md >& ! output.grompp_md

echo "grompp finished"
echo -n "Press <enter>"
set  ans = $<

################
### MDRUN MD ###
################
clear
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
Now we can start the MD simualtion. Watch the number of steps
increasing ( the total number of steps is 2500, for 5 ps ).

-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_

if ( $?DISPLAY ) then
	echo "The output of the mdrun program should appear"  
        echo "in a separate xterm window"
endif

echo -n "Press <enter>"
set  ans = $<

echo "starting mdrun..."
if ( $?DISPLAY ) then 
	xterm -title mdrun -sb -e tail +0f output.mdrun_md &
endif
mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md

echo "mdrun finished"
echo -n "Press <enter>"
set  ans = $<

############
### NGMX ###
############
clear
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
We are finished simulating, and we are going to view the calculated
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
trajectory viewer. 

Once the 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
the box on the left of the word Protein. ( This means that we want to
view the peptide ). Then Click on the OK Button

2. Now we see the edges of the box with a lines drawing of the peptide
we just simulated. 

3. Select Animation in the Display menu. If you did this correctly. A
dialog box at the bottom of the screen appears. This dialog box is
used to move through your trajectory. 

4. Click on the FastForward button (two triangles pointing to the
right) and watch the peptide moving.
-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_

if ( $?DISPLAY ) then
	echo Starting Trajectory viewer...
	ngmx -f ${MOL}_md -s ${MOL}_md  &
endif
#last line