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

structure 	CG_RES_TNF.psf
coordinates	CG_TNF_RBCG_MIN.pdb

set temperature    310

temperature        50

set outputname     CG_TNF_RBCG


# Continuing a job from the restart files
#set inputname      CG_310K
#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	    CG_all_Prot.par

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also 
# specified an .xsc restart file!
#cellBasisVector1     75.     0.     0.
#cellBasisVector2      0.    75.     0.
#cellBasisVector3      0.     0.    65.
#cellOrigin          -20.3   76.8   35.5
#wrapWater           off
#wrapAll             off

# Force-Field Parameters
exclude             none
cutoff              12.0
switching           on
switchdist          10.0
pairlistdist        14.0
hgroupcutoff        0


# Integrator Parameters
timestep            10.0
nonbondedFreq       1
stepspercycle       20


dielectric          78.0

#PME (for full-system periodic electrostatics)
#PME                 yes
#PMEGridSizeX        81
#PMEGridSizeY        81
#PMEGridSizeZ        81

# Constant Temperature Control
langevin            on
langevinDamping     5.0
langevinTemp        $temperature
langevinHydrogen    off

# Constant Pressure Control (variable volume)

#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  1000.
#langevinPistonDecay   500.
#langevinPistonTemp    $temperature

# Output
#binaryoutput        no
outputName          $outputname

restartfreq         10000
dcdfreq             10000
xstFreq             10000
outputEnergies      10000
outputPressure      10000



#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################
# Minimization
minimize            2000
reinitvels $temperature

 run 1000000000