structure mem_wat_ion.psf
coordinates mem_wat_ion.pdb


set prev_run run-0
set new_run  run-1

outputName ./$new_run/$new_run

set temperature    300


firsttimestep      0


# Input
paraTypeCharmm	    on
parameters          ./param/par_all36_lipid.prm
parameters          ./param/par_all36_prot.prm
parameters          ./param/par_all36_carb.prm
parameters          ./param/par_all36_na.prm
parameters          ./param/toppar_water_ions_namd.str
parameters          ./param/par_all36_cgenff.prm



mergeCrossterms yes

temperature         $temperature

# Periodic Boundary conditions
cellBasisVector1     118	0	0
cellBasisVector2     0  	115	0        
cellBasisVector3     0  	0	86      
cellOrigin           0  	0  	0

wrapWater           on
wrapAll             on
wrapNearest         on

tclBC on 
tclBCScript {
  source z_BC.tcl
} 



# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.0
switching           on
switchdist          10.0
pairlistdist        14.0
# margin 3

# Integrator Parameters
timestep            1.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       10




PME                 yes
PMEGridSpacing      1.0



# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     1     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    no    ;# don't couple langevin bath to hydrogens



# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure      no ;# needed for 2fs steps
useFlexibleCell       yes  ;# no for water box, yes for membrane
useConstantArea       yes  ;# no for water box, yes for membrane

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.0
langevinPistonDecay   50.0
langevinPistonTemp    $temperature
}


restartfreq         100     ;# 500steps = every 1ps
dcdfreq             5000
#velDCDfile  		$inputname.veldcd
#velDCDfreq  		100

xstFreq             100
outputEnergies      100
outputPressure      100


# Minimization
if {1} {
minimize            5000
reinitvels          $temperature
}

run 10000000 ;# 10 ns