#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################

structure          ./step5_assembly.xplor.psf
coordinates        ./step5_assembly.pdb

set temperature    310.15 
set outputname     pressure-dir-15-20ns

# Continuing a job from the restart files
if {1} {
set inputname      PO-PE_PG-run3 
binCoordinates     $inputname.restart.coor
binVelocities      $inputname.restart.vel
extendedSystem     $inputname.restart.xsc
}

firsttimestep       0     


#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm      on
parameters          ./par_all36_lipid-water-nacl.prm

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        15.0
margin              8.0


# Integrator Parameters
timestep            2.0  
rigidBonds         all  
useSettle           on
nonbondedFreq       1
fullElectFrequency  2
stepspercycle       10
zeroMomentum        yes


# Constant Temperature Control
langevin            off    
langevinDamping     5     
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

#temperature coupling for temperature coupling
tCouple             on
tCoupleTemp         $temperature


# Periodic Boundary Conditions
#cellBasisVector1     52.       0.              0.
#cellBasisVector2     0.        52.             0.
#cellBasisVector3     0.          0.           56. 
#cellOrigin           0.          0.            0. 

wrapAll             on


# PME (for full-system periodic electrostatics)
# multiples of 2,3,5 & >=dimensions above
PME                 yes
PMEGridSizeX        120  
PMEGridSizeY        120
PMEGridSizeZ        120


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no 
useConstantArea       no 

langevinPiston       on 
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    $temperature


# PRESSURE PROFILE CALCULATIONS
pressureProfile on
pressureProfileSlabs 37 
pressureProfileFreq 2500000
pressureProfileAtomTypes 1

# Output
outputName          $outputname

restartfreq         500
dcdfreq             500
xstFreq             500
outputEnergies      500
#outputPressure      1500000



#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

# Minimization
#minimize            2000
#reinitvels          $temperature

run 2500000