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

# Min. and Eq. of KcsA
# embedded in POPC membrane, ions and water.
# Melting lipid tails. PME, Constant Volume.

#############################################################
## ADJUSTABLE PARAMETERS                                    ##
#############################################################

structure          not_water.psf
coordinates        not_water.pdb
outputName         eq_nvt

set temperature    0
set temperature1   303.15

set cons           0

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

firsttimestep      0


#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################
# Input
paraTypeCharmm	    on
parameters          par_all36_lipid.prm

# NOTE: Do not set the initial velocity temperature if you 
# have also specified a .vel restart file!
temperature         $temperature1
 

# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also 
# specified an .xsc restart file!
if {1} { 
cellBasisVector1    124.475      0.         0.
cellBasisVector2      0.       124.475      0.
cellBasisVector3      0.         0.       113.817
cellOrigin          0.0 0.0 0.0
}
wrapWater           on
wrapAll             on

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0

GBIS                on

cutoff              16.0
switching           on
switchdist          15.0
pairlistdist        18.0


# Integrator Parameters
timestep            1.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       2
fullElectFrequency  4  
stepspercycle       20


#PME (for full-system periodic electrostatics)
if {0} {
PME		yes 
PMEGridSpacing  1.0
}


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     1     ;# damping coefficient (gamma) of 1/ps
langevinTemp        $temperature1

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure      yes ;# needed for 2fs steps
useFlexibleCell       yes  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, yes for membrane
useConstantRatio      yes ;# yes for x/y ratio fixed 
langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  200.
langevinPistonDecay   50.
langevinPistonTemp    $temperature1
}


restartfreq        4     ;# 1000steps = every 1ps
dcdfreq            4
xstFreq            4
outputEnergies     4
outputPressure     4


# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms          on
fixedAtomsFile      fixed.pdb
fixedAtomsCol       B
fixedAtomsForces    on
}

#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################
margin      3





if {$cons == 1} {
        constraints on
        consexp 2
        consref   $ref_umb
        conskfile $ref_umb
        conskcol B
        selectConstraints on
        selectConstrX off
        selectConstrY off
        selectConstrZ on
} else {
        constraints off
}

 

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

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

# Minimization


run 1000 ;# 5.0 ns