# Bpti, modified to implicit solvent
numsteps   50000
outputfreq 5
firststep  0
debug 0

exclude scaled1-4

posfile cbpti.min.pdb
psffile cbpti.psf
parfile par_all27_prot_lipid.inp
temperature 300

seed 1234

#outputs
allenergiesfile bpti.out.energies
finPDBPosFile   bpti.out.pdb
dcdFile         bpti.out.dcd
dodcdfile       true

boundaryConditions vacuum

cellManager Cubic
cellsize 6

removeLinearMomentum  0
removeAngularMomentum 0

eigfile               eigVmBPTISCP

doscpism true

Integrator {
  level 1 NormModeInt {
        cyclelength 1
        fixmodes    2346 #OF 2646
        gamma       20
        seed        1234
        temperature 300
        nve         0
        Berendsen   0
        fdof        0

        force Improper
        force Dihedral
        force Bond
        force Angle

        force CoulombSCPISM
          -algorithm NonbondedCutoff
          -switchingFunction C2
          -switchon 15.0
          -cutoff 20.0

        force CoulombBornRadii
            -algorithm NonbondedCutoff
            -switchingFunction Cutoff
            -bornswitch 2
            -cutoff 5
            -cutoff 5

        force LennardJones
         -algorithm NonbondedCutoff
         -switchingFunction C2
         -switchon 15.0
         -cutoff 20.0

    }
    level 0 NormModeSmplMin {
        timestep 20.0
        minimlim 0.5
        massweight true

        force Improper 
        force Dihedral 
        force Bond 
        force Angle 

        force CoulombSCPISM
          -algorithm NonbondedCutoff
          -switchingFunction C2
          -switchon 5.5
          -cutoff 6.5

        force CoulombBornRadii
            -algorithm NonbondedCutoff
            -switchingFunction Cutoff
            -bornswitch 2
            -cutoff 5
            -cutoff 5

        force LennardJones
         -algorithm NonbondedCutoff
         -switchingFunction C2
         -switchon 5.5
         -cutoff 6.5

    }

}