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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          ../common/protein.psf
coordinates        ../common/protein.pdb

set temperature    310
set outputname     protein_wb_eq

firsttimestep      0


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## SIMULATION PARAMETERS                                   ##
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# Input
paraTypeCharmm	    on
parameters         ../common/par_all27_prot_lipid.inp 
temperature         $temperature


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              10.
switching           on
switchdist          8.
pairlistdist        12.5


# Integrator Parameters
timestep            1.0  ;# 2fs/step
rigidBonds          water  ;# needed for 2fs steps
nonbondedFreq       2
fullElectFrequency  4  
stepspercycle       20
twoAwayX	   yes

#temperature increment
reassignTemp	    25
reassignIncr        5
reassignHold	    310
reassignFreq        1000

# 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    98.27799  0.   0.
cellBasisVector2     0.      82.23699    0.
cellBasisVector3     0.    0       89.43699
cellOrigin         -0.279436558485 -0.418478727341 -0.174910590053 

wrapAll             on


# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSpacing      1.0
#PMEGridSizeX        32
#PMEGridSizeY        32
#PMEGridSizeZ        32
#zeroMomentum	     yes

# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
#useFlexibleCell       no
#useConstantArea       no
#
#langevinPiston        on
#langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
#langevinPistonPeriod  100.
#langevinPistonDecay   50.
#langevinPistonTemp    $temperature


# Output
outputName          $outputname

restartfreq         1000     ;# 500steps = every 1ps
dcdfreq             1000
xstFreq             1000
outputEnergies      1000
outputPressure      1000
outputTiming	    1000


# Fixed Atoms Constraint (set PDB beta-column to 1)
fixedAtoms          on
fixedAtomsFile      ../common/fixed_protein.pdb
fixedAtomsCol       B


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## EXTRA PARAMETERS                                        ##
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## EXECUTION SCRIPT                                        ##
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# Minimization
minimize            1000

run 100000 ;# 1ns