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

# Free energy perturbation
#
#############################################################

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

structure          overlay.psf
coordinates        EQUIL_HPO4_wat.coor 
velocities         EQUIL_HPO4_wat.vel

set temperature    295 

set inputname      EQUIL_HPO4_wat 
set outputname	   test_const


firsttimestep      0

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


# Force-Field Parameters

paraTypeCharmm	    on
parameters          par_satpati_gdp_hpo4.prm


# These are specified by CHARMM

exclude             scaled1-4
1-4scaling          1.0
switching           on

# You have some freedom choosing the cutoff

cutoff              16. ;# may use smaller, maybe 10., with PME
switchdist          15. ;# cutoff - 1. here

# Promise that atom won't move more than 2A in a cycle

pairlistdist        18.  ;# cutoff + 2.
stepspercycle       10   ;# redo pairlists every ten steps

# Integrator Parameters

timestep            2.0  ;# 2fs/step
nonbondedFreq       1    ;# nonbonded forces every step
fullElectFrequency  2    ;# PME only every other step

#Harmonic restraint parameters
rigidBonds      all
rigidTolerance  1.0e-8
#constraints     on
#consref         $inputname.coor
#conskfile       $inputname.reg
#conskcol        B 


# periodic cell
cellBasisVector1  51.5 0 0 
cellBasisVector2  0 51.1 0 
cellBasisVector3  0 0 51.1 
cellOrigin        -0.13 0.03 0.01
extendedSystem     $inputname.xsc
wrapAll            on

# full electrostatics
PME             on
PMEGridSizeX    75
PMEGridSizeY    75 
PMEGridSizeZ    75 

# 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

# pressure control
useGroupPressure      yes           ;# needed for rigid bonds
useFlexibleCell       no            ;# no for water box, yes for membrane
useConstantArea       no            ;# no for water box, maybe for membrane
langevinPiston        on
langevinPistonTarget  1.01325       ;# pressure in bar -> 1 atm
langevinPistonPeriod  200.          ;# oscillation period around 200 fs
langevinPistonDecay   100.          ;# oscillation decay time of 100 fs
langevinPistonTemp    $temperature  ;# coupled to heat bath

#output files
binaryoutput        no
outputName          $outputname     ;# base name for output from this run
restartfreq         50             ;# 50 steps = every 0.1ps
dcdfreq            100 
xstFreq            100
outputEnergies     100             ;# 100 steps = every 0.2 ps
#outputTiming      1000             ;# shows time per step and time to completion

run 50010
##########
#EXECUTION
#########

freeEnergy on
freeEnergyConfig {
urestraint {

dist (LIGA,1,P1) (LIG2,2,MG) kf=20 ref=2.63

}

pmf {
    task = stop
    time = 100 ps
  }

}