firststep 0
numsteps  10

seed 1234

posfile alanine.pdb
psffile alanine.psf
parfile alanine.par
temperature 300 

outputfreq 2
allenergiesfile alanine.equilibrium.energies

boundaryConditions periodic

cellManager Cubic
cellsize    6.5

Integrator {

  level 1 EquilibriumMOLLY {
        cyclelength 6
    force Coulomb -algorithm FullEwald -reciprocal
# using cutoff:
#    force Coulomb
#          -algorithm NonbondedSimpleFull
#	  -switchingFunction ComplementC1
#          -cutoff 6.5
  }

  level 0 Leapfrog {
        timestep 1
    force Improper 
    force Dihedral 
    force Bond 
    force Angle 

    force Coulomb -algorithm FullEwald  -real -correction
    force LennardJones
          -algorithm NonbondedCutoff
          -switchingFunction C2
          -cutoff 6.5
          -cutoff 6.5
	  -switchon 0.1
# using cutoff:
#    force LennardJones Coulomb
#          -algorithm NonbondedCutoff
#          -switchingFunction C2
#          -switchingFunction Shift
#          -cutoff 6.5
#          -cutoff 6.5
#	  -switchon 0.1
  }
}