#ProtoMol configuration file - iSGMD simulation for the gas phase of a methane/ethane mixture

#Paralellization method
parallelMode static

#Molecular system input files and parameters
#temperature 192.37
PSFfile     ethane_methane_100_Pure_Trappe.psf
POSfile     ethane_methane_100_Pure_Trappe.coor.xyz
VELfile     ethane_methane_100_Pure_Trappe.vel.xyz
XSCfile     ethane_methane_100_Pure_Trappe.xsc

#Molecular system output files and parameters
reportonfreq                false 
allenergiesfileoutputfreq   1                      # frequency for reporting energy output to a file
oSGPropertiesfileoutputfreq 1    
screenoutputfreq            1                      # frequency for reporting energy output to the screen
finXYZposfile        ethane_methane_100_o20_Trappe.out.coor.xyz  # final xyz coordinate file name
finXYZvelfile        ethane_methane_100_o20_Trappe.out.vel.xyz   # final xyz velocity file name
finXSCfile           ethane_methane_100_o20_Trappe.out.xsc       # final XSC file name (eXtended System Coordinates)
finPSFfile           ethane_methane_100_o20_Trappe.out.psf       # final PSF file name
allenergiesfile      ethane_methane_100_o20_Trappe.out.txt       # name of output file containing all the energy information
iSGPropertiesfile    ethane_methane_100_o20_Trappe.out.isg.txt   # name of output file containing iSG ensemble information 
                                                                 # (Potential & kinetic energy, P, V, T, # of molecules, and 
                                                                 # the fluctuation in conserved quantity)

#Force field information
PARfile ethane_methane.par
TRANSfile ethane_methane.trans
exclude              scaled1-4
coulombScalingFactor 0.5

#Constraints
angularMomentum      0
comMotion            0
shake                true
rattle               true

# Simulation cell dimensions (these numbers are ignored if an XSCfile is specified)
boundaryConditions   Periodic
cellbasisvector1 30.265 0 0
cellbasisvector2 0 30.265 0
cellbasisvector3 0 0 30.265
cellorigin       0 0 0

#Pairlist parameters
cellManager Cubic
cellsize    15.0

# Pressure and temperature calculations
# molVirialCalc must be set to true, the others are optional
VirialCalc           true
molVirialCalc        true
molecularTemperature true

#timestep parameters
firststep 0
numsteps  250000

# of mixture components
components 2

Integrator {
  level 0 iSGVerlet {
        timestep 1

	# target temperature [K]
        components 2

        # target temperature [K]
	temperature    192.37

	# thermostat time period [fs]
        # NOTE: The smaller tauT is, the stronger the temperature control
        # If tauT is too small (~ 1 fs) the simulation can become unstable
        tauT           50.0

        # target pressure [bar]
	pressure       1.99

        # volume thermostat time period [fs]
        # NOTE: The smaller tauV is, the stronger the temperature control on the barostat
        # If tauV is too small the simulation can become unstable
        tauV           50.0

        # barostat time period [fs]
        # NOTE: The smaller tauP is, the stronger the pressure control
        # If tauV is too small the simulation can become unstable
        tauP           150.0

	# target fugacity fraction [unitless]
        # need (# of components) fugacity fractions and they must sum to 1
	# the first number is the fugacity fraction for ethane
	# and the second number is the fugacity fraction for methane
        fugacityfrac   0.80 0.20

	# chemostat time period [fs]
	# NOTE: The smaller tauD is, the stronger the DeltaMu control
        # If tauD is too small (~ 5.0 fs for methane/ethane) the simulation will be unstable
	tauD           350.0
        lambdaTemp     192.37
        tauL           50.0


    # van der Waals force
    force iSGLennardJones
          -algorithm NonbondedCutoff
          -switchingFunction cutoff
          -cutoff 15.0
  }
}