[gmx-users] Hi..
Navratna Vajpai
navratna.vajpai at unibas.ch
Wed Aug 16 09:55:57 CEST 2006
Hey Mark..
I had attached the file along with the mail. I think you could not
receive it. let me paste the contents and explain it little more.
I am trying to run the simulation in vacuum of a nona peptide. I
managed to get pdb2gmx working and even further the EM working. But
when I tried to do the MD run after a small minimization of protein,
I got an error message after the execution of grompp. The execution
asked for the -n option which indicates for the index file. 1) I
don't know why it asked for?
2) If it ask for is there any way to solv this problem. Actually i
tried using that also. But the error stayed back.
I am also pasting the error after the grompp. Somehow this could not
prepare the input file for the MD run.
3) third question is: I am wondering whether i can start my run just
after the execution of pdb2gmx. Any ways 1) the system is in vacuum
and second while running it for quite long, minimization of energy
will automatically take place.
************************************************************************
******
ERROR:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: readir.c, line: 775
Fatal error:
Group sol not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using
the '-n' option of grompp.
In that case use the '-n' option.
*********************************************************
#!/bin/csh
# this is the demo molecule
setenv MOL ilepep
####################
### INTRODUCTION ###
####################
clear
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
Welcome to the GROMACS demo.
This is a script that takes about 10 min to run.
In this demo we will demonstrate how to simulate Molecular
Dynamics (MD) using the GROMACS software package.
The demo will perform a complete molecular dynamics (MD) simulation
of a small peptide in water. The only input file we need to do this
is a pdb file of a small peptide.
If you have any problems or remarks with respect to this demonstration,
please mail to: gromacs at gromacs.org , or check the resources on
our website http://www.gromacs.org .
-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_
echo -n "Press <enter>"
set ans = $<
#########################
### CHECK ENVIRONMENT ###
#########################
clear
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
Before we you can actually start the GROMACS demo, the programs
must be present in your PATH. This might already be the case if
they are linked to /usr/local/bin. If not, follow the instructions
in the getting started section. If GROMACS is not installed
properly on your computer, contact your system manager.
-----------------------------------------------------------------
-----------------------------------------------------------------
_EOF_
echo -n "Press <enter>"
set ans = $<
###############
### PDB2GMX ###
###############
clear
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
file of our peptide ( .pdb extension ).
Because most pdb files do not contain all hydrogen atoms, the 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 )
-----------------------------------------------------------------
-----------------------------------------------------------------
_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"
endif
echo -n "Press <enter>"
set ans = $<
echo "Starting pdb2gmx"
if ( $?DISPLAY ) then
xterm -title /nmr_apps_DarwinPPC/gromacs/bin/pdb2gmx -sb -e tail +0f
output.pdb2gmx &
endif
echo 1 | /nmr_apps_DarwinPPC/gromacs/bin/pdb2gmx -f ${MOL}.pdb -o $
{MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx
echo "pdb2gmx finished"
echo -n "Press <enter>"
set ans = $<
##############
### GROMPP ###
##############
clear
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
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
system would not be stable because of these high energies.
The standard procedure to remove these close contacts is
Energy Minimisation (EM). Energy minimisation slightly changes the
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
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
simulation (in this case an energy minimisation).
-----------------------------------------------------------------
-----------------------------------------------------------------
_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 energy minimisation parameter file...
cat > em.mdp << _EOF_
title = ${MOL}
cpp = /usr/bin/cpp
define = -DFLEXIBLE
integrator = steep
nsteps = 200
emtol = 100
emstep = 0.01
nstcgsteep = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 10
nstxtcout = 0
xtc-precision = 1000
xtc_grps = Protein
energygrps = Protein
nstlist = 0
ns_type = simple
pbc = no
rlist = 0
coulombtype = Cut-off
rcoulomb = 0
epsilon_r = 1
vdw-type = Cut-off
rvdw = 0
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
Shake-SOR = no
shake-tol = 1e-04
lincs-order = 4
lincs-iter = 4
lincs-warnangle = 30
morse = no
_EOF_
echo "Starting grompp..."
if ( $?DISPLAY ) then
xterm -title /nmr_apps_DarwinPPC/gromacs/bin/grompp -sb -e tail +0f
output.grompp_em &
endif
/nmr_apps_DarwinPPC/gromacs/bin/grompp -f em -c ${MOL} -p ${MOL} -o $
{MOL}_em >& ! output.grompp_em
echo "grompp finished"
echo -n "Press <enter>"
set ans = $<
################
### MDRUN EM ###
################
clear
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.
As the Energy Minimisation is running, watch the output of the
program. The first number ( from left to right ) is the number of the
iteration step. The second number is the step size, which gives an
indication of the change in the system. The third number is the
potential energy of the system. This number starts at a high value and
rapidly drops down, and converges, to a large negative value.
-----------------------------------------------------------------
-----------------------------------------------------------------
_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 energy minimisation mdrun..."
if ( $?DISPLAY ) then
xterm -title /nmr_apps_DarwinPPC/gromacs/bin/mdrun -sb -e tail +0f
output.mdrun_em &
endif
/nmr_apps_DarwinPPC/gromacs/bin/mdrun -nice 0 -s ${MOL}_em -o ${MOL}
_em -c ${MOL}_b4md -v >& ! output.mdrun_em
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
define = -DFLEXIBLE
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000 ; total 2 ps.
nstcomm = 1
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstlist = 10
nstenergy = 125
ns_type = simple
comm_mode = ANGULAR
xtc_precision = 1000
xtc_grps = Protein
energygrps = Protein
rlist = 0
rcoulomb = Cut-off
rvdw = Cut-off
epsilon_r = 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
;Periodic Boundary conditions
pbc = No
; 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 /nmr_apps_DarwinPPC/gromacs/bin/grompp -sb -e tail +0f
output.grompp_md &
endif
/nmr_apps_DarwinPPC/gromacs/bin/grompp -n -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 5000, for 10 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 /nmr_apps_DarwinPPC/gromacs/bin/mdrun -sb -e tail +0f
output.mdrun_md &
endif
/nmr_apps_DarwinPPC/gromacs/bin/mdrun -nice 0 -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...
/nmr_apps_DarwinPPC/gromacs/bin/ngmx -f ${MOL}_md -s ${MOL}_md &
endif
#last line
************************************************************************
**************************************
Best regards
Nav
On Aug 16, 2006, at 9:42 AM, Mark Abraham wrote:
> Navratna Vajpai wrote:
>> Dear All .. I have only recently started the GROMACS package. I
>> want to run a MD simulation in vacuum for 5 ns say. I have tried
>> to edit the demo file which comes with the GROMACS package. but
>> Some how it give an error. Which I am still unable to solve. I am
>> atttaching the file under this. Could any one please help me to
>> move further. I am able to generate the .gro file and am able to
>> run the pdb2gmx.
>
> OK at the moment you've done the analogue of calling the over-
> worked free car mechanic and said "My car is broken, tell me what's
> wrong". They are going to be much more likely to give you useful
> help if you tell them what you were trying to do, how you were
> trying to do it, and what the error was when you tried. Otherwise,
> they'll go and do something more interesting and/or profitable. :-)
>
> Mark
> _______________________________________________
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*******************************************
Navratna Vajpai
Ph. D student in Prof. Grzesiek's laboratory
Department of Structural Biology
Biozentrum, University of Basel
Klingelbergstrasse 70,
CH-4056
Basel, Switzerland.
Phone- +41 61 267 2080(O)
+41 78 744 0810(M)
navratna.vajpai at unibas.ch
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