Team:EPF-Lausanne/Modeling/NamdConf

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=Job description=
=Job description=
Line 13: Line 26:
: # 14:00
: # 14:00
: # Nicolas Gobet
: # Nicolas Gobet
 +
 +
=Adjustable parameters=
=Adjustable parameters=
==First run==
==First run==
-
==Resume after previous complete run==
+
This is an example for the heating.
 +
: #############################################################
 +
: ## ADJUSTABLE PARAMETERS                                  ##
 +
: #############################################################
 +
 
 +
:structure          ./2v0up_wb_i.psf
 +
:coordinates        ./2v0up_wb_i.pdb
 +
 
 +
:set paramfich    ./common/par_all27_prot_lipid-fmn_dark.prm
 +
 
 +
:set temperature    300
 +
 
 +
: #initial temperature
 +
:temperature        $temperature
 +
 
 +
:set outputdir        ./output_eq3
 +
 
 +
:set outputname      $outputdir/2v0up_wb_i_eq
 +
:set outputmin        $outputdir/min
 +
:set outputheating    $outputdir/heating
 +
:set outputnpt1      $outputdir/NPT_1
 +
:set outputnvt        $outputdir/NVT_1
 +
:set outputnpt2      $outputdir/NPT_2
 +
 
 +
 
 +
 
 +
==Resume from .coord, .vel, .xsc==
 +
This is to resume from .coor, .vel and .xsc files. As we load velocities and positions from a file, we don't have to set initial temperature, load .pdb for postions of the atoms and set parameters such as box size
 +
: #############################################################
 +
: ## ADJUSTABLE PARAMETERS                                  ##
 +
: #############################################################
 +
 
 +
:structure          ./2v0up_wb_i.psf
 +
:set paramfich    ./common/par_all27_prot_lipid-fmn_dark.prm
 +
 
 +
:set temperature 300
 +
 
 +
:set inputdir        ./output_eq2
 +
:set inputname      2v0up_wb_i_eq
 +
 
 +
:coordinates $inputdir/$inputname.coor
 +
:velocities $inputdir/$inputname.vel
 +
:extendedSystem  $inputdir/$inputname.xsc
 +
 
 +
:set outputdir        ./output_sim2
 +
 
 +
:set outputname      $outputdir/2v0up_wb_i_sim
 +
:set outputsim        $outputdir/min
 +
 
 +
 
 +
 
 +
=Simulation parameters=
 +
==First run==
 +
This part is from a heating .conf. The size of the box and origin has to be adjusted.
 +
PMEGridSize parameters have to be adjusted to be higher than the size of the box and be a multiple of 2, 3 and 5. (please refer to tutorial)
 +
: #############################################################
 +
: ## SIMULATION PARAMETERS                                  ##
 +
: #############################################################
 +
 
 +
:firsttimestep      0
 +
 
 +
: # Input
 +
:paraTypeCharmm     on
 +
:parameters          $paramfich
 +
 
 +
 
 +
: # Force-Field Parameters
 +
:exclude            scaled1-4
 +
:1-4scaling          1.0
 +
:cutoff              12.
 +
:switching          on
 +
:switchdist          10.
 +
:pairlistdist        13.5
 +
 
 +
 
 +
: # Integrator Parameters
 +
: # '''We use timestep of 2.0 only for heating!!!!!!''' Any other case is 1.0
 +
:timestep            '''2.0'''
 +
:rigidBonds          all  ;# needed for 2fs steps
 +
:nonbondedFreq      1
 +
:fullElectFrequency  2 
 +
:stepspercycle      10 
 +
 
 +
: # Constant Temperature Control
 +
:langevin            on    ;# do langevin dynamics
 +
:langevinDamping    $temperature    ;# damping coefficient (gamma) of 5/ps
 +
:langevinTemp        $temperature # je viens de changer, foiruex avant
 +
:langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
 +
 
 +
 
 +
: # Periodic Boundary Conditions
 +
:'''cellBasisVector1    63.39    0.  0.'''
 +
:'''cellBasisVector2    0.  65.404  0.'''
 +
:'''cellBasisVector3    0.    0  69.675'''
 +
:'''cellOrigin          14.1049346924  3.42041158676  3.65775823593'''
 +
 
 +
:wrapAll            on
 +
 
 +
 
 +
: # PME (for full-system periodic electrostatics)
 +
:PME                yes
 +
:'''PMEGridSizeX        66'''
 +
:'''PMEGridSizeY        66'''
 +
:'''PMEGridSizeZ        70'''
 +
 
 +
 
 +
: # Constant Pressure Control (variable volume)
 +
:useGroupPressure      yes ;# needed for rigidBonds
 +
:useFlexibleCell      no ;# no for water box
 +
:useConstantArea      no ;# no for water box
 +
 
 +
:langevinPiston        on
 +
:langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
 +
:langevinPistonPeriod  200.
 +
:langevinPistonDecay  100.
 +
:langevinPistonTemp    $temperature
 +
 
 +
 
 +
: # Output
 +
:outputName          $outputname
 +
 
 +
:restartfreq        500    ;# 500steps = every 1ps
 +
:dcdfreq            200
 +
:xstFreq            200
 +
:outputEnergies      200
 +
:outputPressure      200
 +
:outputTiming      200
 +
:binaryoutput     off
 +
 
 +
 
 +
 
 +
==Resume from .coord, .vel, .xsc==
 +
The only difference here is that we lower timestep for NPT simulation to copy parameters from Schulten's paper. Then, we don't set the size of the water box as it is loaded from the file and we lower the frequency of output.
 +
This is what you have to copy for a NPT simulation.
 +
: #############################################################
 +
: ## SIMULATION PARAMETERS                                  ##
 +
: #############################################################
 +
 
 +
:firsttimestep      0
 +
 
 +
: # Input
 +
:paraTypeCharmm     on
 +
:parameters          $paramfich
 +
 
 +
 
 +
: # Force-Field Parameters
 +
:exclude            scaled1-4
 +
:1-4scaling          1.0
 +
:cutoff              12.
 +
:switching          on
 +
:switchdist          10.
 +
:pairlistdist        13.5
 +
 
 +
 
 +
: # Integrator Parameters
 +
:'''timestep            1.0'''
 +
:rigidBonds          all  ;# needed for 2fs steps
 +
:nonbondedFreq      1
 +
:fullElectFrequency  2 
 +
:stepspercycle      10 
 +
 
 +
: # Constant Temperature Control
 +
:langevin            on    ;# do langevin dynamics
 +
:langevinDamping    $temperature    ;# damping coefficient (gamma) of 5/ps
 +
:langevinTemp        $temperature # je viens de changer, foiruex avant
 +
:langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
 +
 
 +
 
 +
: # Periodic Boundary Conditions
 +
:wrapAll            on
 +
 
 +
 
 +
: # PME (for full-system periodic electrostatics)
 +
:PME                yes
 +
:PMEGridSizeX        50
 +
:PMEGridSizeY        54
 +
:PMEGridSizeZ        60
 +
 
 +
 
 +
: # Constant Pressure Control (variable volume)
 +
:useGroupPressure      yes ;# needed for rigidBonds
 +
:useFlexibleCell      no ;# no for water box
 +
:useConstantArea      no ;# no for water box
 +
 
 +
:langevinPiston        on
 +
:langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
 +
:langevinPistonPeriod  200.
 +
:langevinPistonDecay  100.
 +
:langevinPistonTemp    $temperature
 +
 
 +
 
 +
: # Output
 +
:outputName          $outputname
 +
 
 +
:restartfreq        2000    ;# 500steps = every 1ps
 +
:dcdfreq            2000
 +
:xstFreq            2000
 +
:outputEnergies      2000
 +
:outputPressure      2000
 +
:outputTiming      2000
 +
:binaryoutput     off
 +
 
 +
 
 +
 
 +
=Execution script=
 +
==Heating==
 +
: #############################################################
 +
: ## EXECUTION SCRIPT                                        ##
 +
: #############################################################
 +
 
 +
: # run one step to get into scripting mode
 +
:minimize 0
 +
 
 +
: # turn off until later
 +
:langevinPiston off
 +
 
 +
: # Minimization
 +
:minimize            2500
 +
:reinitvels          5
 +
:output $outputmin
 +
 
 +
: # heating NPT
 +
: # langevin on
 +
:for {set i 5} {$i <= $temperature} {incr i 5} { ;# i = 5, $i<300, incr i = 5
 +
:set temperaturei $i
 +
:langevinTemp $temperaturei
 +
:langevinPistonTemp $temperaturei
 +
:run 2000 ;# run 2000
 +
:}
 +
 
 +
: #to be sure we are at the right temperature
 +
:langevinTemp $temperature
 +
:langevinPistonTemp $temperature
 +
 
 +
:output $outputheating
 +
 
 +
: # 1st equilibrate pression
 +
: # NPT equilibration
 +
: # langevin on
 +
:langevinPiston on
 +
:run 50000 ;# run 50000
 +
:output $outputnpt1
 +
 
 +
: # NVT equilibration
 +
: # langevin off
 +
:langevinPiston off
 +
:run 50000 ;# run 50000
 +
:output $outputnvt
 +
 
 +
: # NPT equilibration
 +
:langevinPiston on
 +
:run 150000 ;# run 150000
 +
:output $outputnpt2
 +
 
 +
 
 +
 
 +
==NPT run==
 +
: #############################################################
 +
: ## EXECUTION SCRIPT                                        ##
 +
: #############################################################
 +
 
 +
: # run one step to get into scripting mode
 +
: #minimize 0
 +
 
 +
: # NPT equilibration
 +
: # langevin on
 +
: #langevinPiston on
 +
:run 1000000 ;# run 1 ns
 +
:output $outputsim
 +
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Latest revision as of 13:32, 21 October 2009


Job description

This section is needed are we trying to keep track of each run, please put type of simulation, pdb loaded, date, time and your name

#############################################################
## JOB DESCRIPTION ##
#############################################################
# NPT simul
# 2v0u in a water box
# 12.08.09
# 14:00
# Nicolas Gobet


Adjustable parameters

First run

This is an example for the heating.

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ./2v0up_wb_i.psf
coordinates ./2v0up_wb_i.pdb
set paramfich ./common/par_all27_prot_lipid-fmn_dark.prm
set temperature 300
#initial temperature
temperature $temperature
set outputdir ./output_eq3
set outputname $outputdir/2v0up_wb_i_eq
set outputmin $outputdir/min
set outputheating $outputdir/heating
set outputnpt1 $outputdir/NPT_1
set outputnvt $outputdir/NVT_1
set outputnpt2 $outputdir/NPT_2


Resume from .coord, .vel, .xsc

This is to resume from .coor, .vel and .xsc files. As we load velocities and positions from a file, we don't have to set initial temperature, load .pdb for postions of the atoms and set parameters such as box size

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ./2v0up_wb_i.psf
set paramfich ./common/par_all27_prot_lipid-fmn_dark.prm
set temperature 300
set inputdir ./output_eq2
set inputname 2v0up_wb_i_eq
coordinates $inputdir/$inputname.coor
velocities $inputdir/$inputname.vel
extendedSystem $inputdir/$inputname.xsc
set outputdir ./output_sim2
set outputname $outputdir/2v0up_wb_i_sim
set outputsim $outputdir/min


Simulation parameters

First run

This part is from a heating .conf. The size of the box and origin has to be adjusted. PMEGridSize parameters have to be adjusted to be higher than the size of the box and be a multiple of 2, 3 and 5. (please refer to tutorial)

#############################################################
## SIMULATION PARAMETERS ##
#############################################################
firsttimestep 0
# Input
paraTypeCharmm on
parameters $paramfich


# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5


# Integrator Parameters
# We use timestep of 2.0 only for heating!!!!!! Any other case is 1.0
timestep 2.0
rigidBonds all  ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on  ;# do langevin dynamics
langevinDamping $temperature  ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature # je viens de changer, foiruex avant
langevinHydrogen off  ;# don't couple langevin bath to hydrogens


# Periodic Boundary Conditions
cellBasisVector1 63.39 0. 0.
cellBasisVector2 0. 65.404 0.
cellBasisVector3 0. 0 69.675
cellOrigin 14.1049346924 3.42041158676 3.65775823593
wrapAll on


# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 66
PMEGridSizeY 66
PMEGridSizeZ 70


# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no ;# no for water box
useConstantArea no ;# no for water box
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature


# Output
outputName $outputname
restartfreq 500  ;# 500steps = every 1ps
dcdfreq 200
xstFreq 200
outputEnergies 200
outputPressure 200
outputTiming 200
binaryoutput off


Resume from .coord, .vel, .xsc

The only difference here is that we lower timestep for NPT simulation to copy parameters from Schulten's paper. Then, we don't set the size of the water box as it is loaded from the file and we lower the frequency of output. This is what you have to copy for a NPT simulation.

#############################################################
## SIMULATION PARAMETERS ##
#############################################################
firsttimestep 0
# Input
paraTypeCharmm on
parameters $paramfich


# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5


# Integrator Parameters
timestep 1.0
rigidBonds all  ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on  ;# do langevin dynamics
langevinDamping $temperature  ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature # je viens de changer, foiruex avant
langevinHydrogen off  ;# don't couple langevin bath to hydrogens


# Periodic Boundary Conditions
wrapAll on


# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 50
PMEGridSizeY 54
PMEGridSizeZ 60


# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no ;# no for water box
useConstantArea no ;# no for water box
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature


# Output
outputName $outputname
restartfreq 2000  ;# 500steps = every 1ps
dcdfreq 2000
xstFreq 2000
outputEnergies 2000
outputPressure 2000
outputTiming 2000
binaryoutput off


Execution script

Heating

#############################################################
## EXECUTION SCRIPT ##
#############################################################
# run one step to get into scripting mode
minimize 0
# turn off until later
langevinPiston off
# Minimization
minimize 2500
reinitvels 5
output $outputmin
# heating NPT
# langevin on
for {set i 5} {$i <= $temperature} {incr i 5} { ;# i = 5, $i<300, incr i = 5
set temperaturei $i
langevinTemp $temperaturei
langevinPistonTemp $temperaturei
run 2000 ;# run 2000
}
#to be sure we are at the right temperature
langevinTemp $temperature
langevinPistonTemp $temperature
output $outputheating
# 1st equilibrate pression
# NPT equilibration
# langevin on
langevinPiston on
run 50000 ;# run 50000
output $outputnpt1
# NVT equilibration
# langevin off
langevinPiston off
run 50000 ;# run 50000
output $outputnvt
# NPT equilibration
langevinPiston on
run 150000 ;# run 150000
output $outputnpt2


NPT run

#############################################################
## EXECUTION SCRIPT ##
#############################################################
# run one step to get into scripting mode
#minimize 0
# NPT equilibration
# langevin on
#langevinPiston on
run 1000000 ;# run 1 ns
output $outputsim


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