#############################################################
## JOB DESCRIPTION                                         ##
#############################################################

# The task of this configuration file is NPT run after pre-Eq. run 


#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################
set import sbox_init 
#set minim energy-minimization
#set export EM1
#set init_temp 0
set desired_temp 330 
structure                    ${import}.psf
coordinates                  ${import}.pdb
bincoordinates               310K-init.coor  ; # from pre-eq 
extendedSystem               310K-init.xsc

# Continuing a job from the restart files
#if {0} {
#set inputname                myinput
#binCoordinates               $inputname.restart.coor
#binVelocities                $inputname.restart.vel ; #remove "temperature" entry if you use this!
#extendedSystem               $inputname.restart.xsc
#}

firsttimestep                0
numsteps                     500   ; # 20 ns

outputName                   const_j1_310K

#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

#forcefield parameter file (AMBER99bs0)
paraTypeCharmm               on
parameters                   parm99bs0_all.prm

# NOTE: Do not set the initial velocity temperature if you 
# have also specified a .vel restart file!
#initial config
temperature                  $desired_temp

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also 
# specified an .xsc restart file!
# cellBasisVector1    70.872001648    0.   0.
# cellBasisVector2     0.   97.295000493545   0.
# cellBasisVector3     0.    0   87.7749958039
# cellOrigin           55.5835037231   48.3113365173   23.6531543732
wrapWater           on
wrapAll             on

# Force-Field Parameters
exclude                      scaled1-4
1-4scaling                   1.0
cutoff                       12.0
switching                    on
switchdist                   10.0
pairlistdist                 13.5


#integrator parameters
timestep                     2.0
rigidBonds                   all
nonbondedFreq                1

#outputfiles and restart options
# outputname                   ${export}
binaryoutput                 no
restartname                  restart
restartfreq                  500
binaryrestart                yes
dcdfreq                      10000   ;# 20 ps interval 
xstfreq                      250
outputEnergies               1000
outputTiming                 1000
outputPressure               1000

# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX         72
PMEGridSizeY         97
PMEGridSizeZ         89

#Fixed atoms for initial heating up steps
#fixedAtoms on
#fixedAtomsForces on
#fixedAtomsFile fix_solute.pdb
#fixedAtomsCol B

#Restrained atoms for initial heating-up
#constraints                  on
#consref                      fix_solute.pdb
#conskfile                    fix_solute.pdb
#conskcol                     B

# Constant Temperature Contro
langevin              on
langevinDamping       5.
langevinTemp          $desired_temp
langevinHydrogen      no


#langevin pressure control
useGroupPressure      yes ;# needed for 2fs steps
useFlexibleCell       no  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, yes for membrane

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

run 500


#Temperature reassignment
#reassignFreq 10000
#reassignTemp  $init_temp
#reassignIncr 10
#reassignHold $desired_temp

#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################

# Put here any custom parameters that are specific to 
# this job (e.g., SMD, TclForces, etc...)

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

#Minimization

#run 1 step to get into scripting mode
#minimize 0

#turn off pressure control until later
#langevinPiston off

#fix solute
#minimize 1000

#minimize all atoms
#fixedAtoms off
#minimize 1000

#Heat gradually 10K/1000steps
#reinitvels $init_temp
#run 600000

#equilibrate volume with Ps restrained
#langevinPiston        on
#run 600000; #12ns

#equilibrate volume without restraints
#constraintScaling 0
#run 6000000; #120ns