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

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## JOB DESCRIPTION ##

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# 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.

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## ADJUSTABLE PARAMETERS ##

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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

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## ADJUSTABLE PARAMETERS ##

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structure ./2v0up_wb_i.psf

set paramfich ./common/par_all27_prot_lipid-fmn_dark.prm

set temperature 300

set inputdir ./output_eq2

coordinates $inputdir/2v0up_wb_i_eq.coor

velocities $inputdir/2v0up_wb_i_eq.vel

extendedSystem $inputdir/2v0up_wb_i_eq.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)

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## SIMULATION PARAMETERS ##

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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.

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## SIMULATION PARAMETERS ##

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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

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## EXECUTION SCRIPT ##

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# 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

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## EXECUTION SCRIPT ##

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# run one step to get into scripting mode

#minimize 0

# NPT equilibration

# langevin on

#langevinPiston on

run 1000000 ;# run 1 ns

output $outputsim