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

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

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

# Continuing a job from the restart files
if {1} {
set inputname      PO-PE_PG-run3               ;# these are the outputs till 15ns
binCoordinates     $inputname.restart.coor
binVelocities      $inputname.restart.vel
extendedSystem     $inputname.restart.xsc
}


#############################################################
## 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



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


outputName          $outputname

#finding pressure profile
pressureProfile        on
pressureProfileSlabs   37 
pressureProfileFreq   2500000             ;# writing PRESSUREPROFILE at the begining and at the end
pressureProfileAtomTypes 1
pressureProfileEwald on
pressureProfileEwaldX 15
pressureProfileEwaldY 15
pressureProfileEwaldZ 15
set ts 0
firstTimestep $ts
coorfile open dcd ./pressure-dir-15-20ns.dcd          ;# this is the dcd output of pressure calculations run (bonded,..)
while { [coorfile read] != -1 } {
  incr ts 500                              ;# dcd was written every 500 steps
  firstTimestep $ts
  run 0
}
coorfile close