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## JOB DESCRIPTION                                         ##
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# NVT run of 500 molecules of ethanol  
# for time interval of t_start to t_end ns.


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## ADJUSTABLE PARAMETERS                                   ##
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structure          ../../common/final.psf
coordinates        coorname
extendedSystem	   xscname
velocities	   velname

set temperature    300
set outputname     output_name
set restart	   0

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

firsttimestep      ts_first


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

# Input
paraTypeCharmm	    on
parameters          ../../common/final.params 
if {0} {
temperature         $temperature
}

# Force-Field Parameters
#dielectric         80
exclude             scaled1-4
nonbondedScaling    0.833
1-4scaling          0.5
cutoff              12.0
switching           on
switchdist          10.5
pairlistdist        13.5

# Integrator Parameters
timestep            2.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
vdwGeometricSigma   yes
fullElectFrequency  2  
stepspercycle       20
pairlistsperCycle   2

# Periodic Boundary Conditions
if {0} {
cellBasisVector1    45.0    0.0    0.0
cellBasisVector2     0.0   45.0    0.0
cellBasisVector3     0.0    0.0   90.0
cellOrigin          22.5   22.2  42.5


# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSpacing      1.0

#manual grid definition
#PMEGridSizeX        45
#PMEGridSizeY        45
#PMEGridSizeZ        90
}
wrapAll             on

# Constant Temperature Control
if {1} {
langevin            on    ;# do langevin dynamics
langevinDamping     1     ;# damping coefficient (gamma) of 1/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
}

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.0
langevinPistonDecay   50.0
langevinPistonTemp    $temperature
}

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms          on
fixedAtomsFile      ../STEP1/final_eq1.coor
fixedAtomsCol       B
}

# IMD Settings (can view sim in VMD)
if {0} {
IMDon           on
IMDport         3000    ;# port number (enter it in VMD)
IMDfreq         1       ;# send every 1 frame
IMDwait         no      ;# wait for VMD to connect before running?
}

# Output
outputName          $outputname
XSTfile             $outputname.xst


restartfreq         5000     ;# 500steps = every 1ps
dcdfreq             5000
XSTfreq             5000
outputEnergies      1000
outputPressure      1000

binaryoutput		no
binaryrestart		no

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


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## EXECUTION SCRIPT                                        ##
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# Equilibration
numsteps			ts_end				# Number of integration steps