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## JOB DESCRIPTION                                         ##
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# Minimization and Equilibration of 
# Ubiquitin in a Water Box


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## ADJUSTABLE PARAMETERS                                   ##
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structure         glycop_128_mix_w32.psf
coordinates       glycop_128_mix_w32.pdb

set temperature    320
set outputname     ./NPT_13/glycop_128_mix_w32

#start parametrs

set inputname       ./NPT_12/glycop_128_mix_w32
binCoordinates     $inputname.restart.coor
binVelocities      $inputname.restart.vel  ;# remove the "temperature" entry if you use this!
extendedSystem     $inputname.restart.xsc

firsttimestep    11000000



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## SIMULATION PARAMETERS                                   ##
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# Input
paraTypeCharmm      on
parameters          par_all27_prot_lipid.prm
#temperature         $temperature


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        13.5


# Integrator Parameters
timestep            2.0  ;# 2fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       2


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens


# Periodic Boundary Conditions
#cellBasisVector1    77.7  0.    0.
#cellBasisVector2     0.  77.4   0.
#cellBasisVector3     0.   0.   70.1
cellOrigin          77.5  82.5 -13.9

wrapAll             on
wrapWater 	     on
#rigidDieOnError     off

# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX        50
PMEGridSizeY        50
PMEGridSizeZ        50


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

#SurfaceTensionTarget 5

#selecting constrains for moving only in xy plane
#selectConstraints   on
#selectConstrZ	    on

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


# Output
outputName          $outputname
binaryoutput        no


restartfreq         25000     ;# 500steps = every 1ps
dcdfreq             25000
xstFreq             500
#velDCDfile	    $inputname.vel.dcd
#velDCDfreq	    25000

outputEnergies      500
outputPressure      500


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## EXTRA PARAMETERS                                        ##
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#margin 55

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## EXECUTION SCRIPT                                        ##
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# Minimization
#minimize            100
reinitvels          $temperature

run  3000000  ; # 10ps