temperature 300.0 
firststep 0

numsteps 10000

cellsize 6.5


outputfreq 100
seed 1234



posfile alanin.pdb
psffile alanin.psf
parfile alanin.par

dofinXYZPosFile alanin.out.pos.xyz
dofinXYZVelFile alanin.out.vel.xyz
dcdfile alanin.out.dcd
allenergiesfile alanin.out.energy



boundaryConditions Normal
cellManager Cubic


Integrator {
  level 0 Leapfrog {
        timestep 1
    force Improper 
    force Dihedral 
    force Bond 
    force Angle 
    force LennardJones
          -algorithm NonbondedCutoff
          -switchingFunction C2
	  -switchon 1.0
          -cutoff 12
    force Coulomb
          -algorithm NonbondedCutoff
          -switchingFunction C1
          -cutoff 12
    force Haptic
	  -port 2001
	  -trate 1
	  -timeout 1000
	  -step_inc 100
	  -wait 0
  }
}