proc get_first_ts { xscfile } {
  set fd [open $xscfile r]
  gets $fd
  gets $fd
  gets $fd line
  set ts [lindex $line 0]
  close $fd
  return $ts
}

#############################################################
## JOB DESCRIPTION                                         ##
#############################################################
#
# Initial minimization of the coarse-grained system.
#
#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################
set inputname    pr  
set outputname  min-nocons 

set temperature    300
cosAngles          on

structure 	 sim.psf
coordinates	 sim.pdb
#temperature      $temperature

bincoordinates  $inputname.restart.coor
binvelocities   $inputname.restart.vel
extendedSystem  $inputname.restart.xsc
COMMotion       yes



firsttimestep   0
 
#############################################################
## SIMULATION PARAMETERS                                   ## 
#############################################################

# Input
paraTypeCharmm	    on
parameters          pace-reopt.prm
parameters          martini_v2.0_lipids.prm
parameters          martini_v2.0_ions.prm

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.0
switching           on
switchdist          9.0
pairlistdist        12.0
dielectric          15.0




# Integrator Parameters
timestep            2.0
nonbondedFreq       1 
stepspercycle       10

# Constant Temperature Control
langevin            yes    ;# do langevin dynamics
langevinDamping     0.5      ;# damping coefficient (gamma) of 1/ps
langevinTemp        $temperature
langevinHydrogen    on    ;# don't couple langevin bath to hydrogens

# Periodic Boundary CondiAions
if {0} {
cellBasisVector1   105.0  0       0
cellBasisVector2   0       110.0  0
cellBasisVector3   0       0      100.0 
cellOrigin        0.00  0.00   0.00     
}
wrapAll             on

# Constant Pressure Control (variable volume)
useGroupPressure      no
useFlexibleCell       yes
useConstantArea       no
useConstantRatio      no 

langevinPiston        yes
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  200.  #usually 2000 for RBCG system 
langevinPistonDecay   100.  #usually 1000 for RBCG system
langevinPistonTemp    $temperature

# Output
outputName          $outputname
restartfreq          100   
dcdfreq              1000
xstFreq              1000
outputEnergies       100
outputPressure       100





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

minimize             2500
run                  10000