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## JOB DESCRIPTION                                         ##
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# Minimization and Equilibration of 
#  a glucose water Box


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## ADJUSTABLE PARAMETERS                                   ##
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structure          Solute2Solvent-10.psf
coordinates        Solute2Solvent-10.pdb

set temperature    300
set pressure       1.01325
set outputname     glucose-water-10-300

firsttimestep      0


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## SIMULATION PARAMETERS                                   ##
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# Input
paraTypeCharmm	    on
parameters          par_all36_carb.prm
#set velocities
seed                12345678
temperature         $temperature


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        13.5
margin              10
splitPatch          hydrogen
#Atoms outside pairlistdist will stay outside cutoff for 10 steps
stepspercycle       10 


# Integrator Parameters
timestep            2.0  ;# 2fs/step
#相当于LAMMPS里面的fix shake,如果useSettle on,不用shake
rigidBonds          all  ;# needed for 2fs steps
rigidIterations     50
rigidTolerance      1e-8
useSettle           off
nonbondedFreq       1
fullElectFrequency  2  
  


# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens


# Periodic Boundary Conditions
cellBasisVector1    36.72999954223633    0.   0.
cellBasisVector2     0.    47.84199905395508    0.
cellBasisVector3     0.    0   59.3380012512207
cellOrigin         18.28191566467285 24.04880142211914 29.60899543762207

wrapAll             on

# PME (for full-system periodic electrostatics)
PME                 yes
PMETolerance        1e-6
PMEGridSizeX        64
PMEGridSizeY        64
PMEGridSizeZ        64


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

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


# Output
outputName          $outputname
binaryoutput        no
binaryrestart       no
restartfreq         500     ;# 500steps = every 1ps
dcdfreq             250
velDCDFreq          1000
xstFreq             250
outputEnergies      100
outputPressure      100


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## EXTRA PARAMETERS                                        ##
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## EXECUTION SCRIPT                                        ##
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# Minimization
minimize            1000
reinitvels          $temperature

run 500000 ;# 2ns