#JOB DESCRIPTION                                         ##
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# dapc equilibration


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## ADJUSTABLE PARAMETERS                                   ##
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structure    xxx.psf 
coordinates  xxx.pdb
#binvelocities min_mem.vel

#set start_temperature   x
set hold_temperature    x
set outputname min_mem.md

firsttimestep      0


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## SIMULATION PARAMETERS                                   ##
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# Input
paraTypeCharmm      on
parameters          p.prm
temperature         x


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              14.0
switching           on
switchdist          12.0 #Cutoff-2
pairlistdist        16.0  #Cutoff+2
stepspercycle       10
margin 2.5


# Integrator Parameters
timestep            2.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2
useSettle           on   ;#If rigid bonds are enabled use
#non-interactive SETTLE alg to keep waters rigid


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinHydrogen    no    ;# don't couple langevin bath to hydrogens
langevinTemp        x ;#langevin temperature is
#defined in protocol section

#Affects the output. Wrapping does not affect the simulation.
wrapWater           on
wrapAll             on


#Pressure Control
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

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

# Periodic Boundary Conditions
cellBasisVector1 96.87   0   0
cellBasisVector2 0   74.57   0
cellBasisVector3 0    0   110.68
cellOrigin 0.0   0.0   0.0

#PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSpacing      1.0 ;#Using good default. Let NAMD set the grid.

PMEGridSizeX        100  
PMEGridSizeY        80
PMEGridSizeZ        120 

# Output
binaryoutput	   on
outputName         xx

restartfreq 2500
dcdfreq 2500
xstFreq 2500
outputEnergies 2500
outputPressure 2500


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## EXTRA PARAMETERS                                        ##
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constraints off

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## EXECUTION SCRIPT                                        ##
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# Minimization # ( 20 ps )
minimize            10000

# heat with CAs restrained
# langevin	on
run 3000
output heat 

#RELAXATION PROTOCOL
#35000 steps
# 14 frames (dcdfreq=2500)
# 70 ps     (timestep=2fs)

# Heat +1K in 0.4ps
#for { set TEMP 0 } { $TEMP < x } {
#incr TEMP 1 } {
#       langevinTemp x
#       reinitvels x
#       run 200
#}

#Adjust environment to final conditions
langevinTemp x
reinitvels x

#Constraints release protocol


#Free dynamics for 50 ps
constraintScaling 0
run 25000