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## JOB DESCRIPTION                                         ##
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# Minimization of 500 molecules of ethanol


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## ADJUSTABLE PARAMETERS                                   ##
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#specify the location of the psf and pdb files
structure          ../common/final.psf
coordinates        ../common/final.pdb

# specify the temperature here 
set temperature    0
set outputname     final_min

# in case you are restarting a run, put restart =1, otherwise we set restart =0
set restart	   0

# this loop won't run, as our restart variable is set to 0
# Continuing a job from the restart files
if {$restart} {
set inputname      $outputname
Coordinates        ../$inputname.restart.coor
Velocities         ../$inputname.restart.vel  ;# remove the "temperature" entry if you use this!
extendedSystem	   ../$inputname.restart.xsc
} 

# firsttimestep is a command, not a variable, so we don't use 'set' here
firsttimestep      0


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## SIMULATION PARAMETERS                                   ##
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# Input

# specify the parameter files location
paraTypeCharmm	    on
parameters          ../common/final.params
# this loop won't work
if {$restart-1} {
temperature	    $temperature
}

# Force-Field Parameters
# these parameters are usually fixed for Charmm ff
exclude             scaled1-4
1-4scaling          0.5
switching           on

# the next 4 parameters can be edited as per your CPU power and time

# beyond cutoff electrostatics interactions aren't calculated;
cutoff              12.0

# switchdist and pairlistdist keep a track on the atoms moved
# they basically control that the atom doesn't move 
# arbitrarily far in one step
switchdist          10.5
pairlistdist        13.5

# stepspercycle is the number of cycles after which namd will 
# update the pairlistdist  
stepspercycle       20

# Integrator Parameters
timestep            2.0
rigidBonds          all
nonbondedFreq       1
vdwGeometricSigma   yes
fullElectFrequency  2  
pairlistsperCycle   2

# Periodic Boundary Conditions
if {$restart-1} {
cellBasisVector1    45.0    0.   0.0
cellBasisVector2     0.0  45.0   0.0 
cellBasisVector3     0.0    0    90.0
cellOrigin          22.529 22.236 43.510

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

#manual grid definition
#PMEGridSizeX        45
#PMEGridSizeY        45
#PMEGridSizeZ        100
}
wrapAll             on

# Constant Temperature Control
if {0} {
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
fixedAtomsForces    on #Is it necessary?
fixedAtomsFile      myfixedatoms.pdb
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
# all output files will have the same name but different extensions
# our outputname is final_min, so
# final_min.dcd final_min.coor etc files will be created

outputName          $outputname

# 1 step = 2 fs
# 500 step = 1000 fs = 1 ps
# remember : 1 step = 2 fs; 1000fs = 1ps and 1000ps = 1ns
# remember : 1ns = 1000ps and 1ps = 1000fs
# MD Simulations are run for 40-60 ns range
# so steps = 40*1000*1000/2 = (time/2)*10^6 steps

restartfreq         500
dcdfreq             200
outputEnergies      100
outputPressure      100

binaryoutput		no
binaryrestart		no

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## EXTRA PARAMETERS                                        ##
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## EXECUTION SCRIPT                                        ##
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# Minimization
minimize            10000