temperature 300.0 
firststep 0

numsteps 10000

cellsize 6.5


outputfreq 100
restartfreq 1000      
seed 1234



posfile alanin.pdb
psffile alanin.psf
parfile alanin.par
usecharmm28parfile no

finpdbposfile alanin.out.pos.pdb
finpdbvelfile alanin.out.vel.pdb
dcdfile alanin.out.dcd
allenergiesfile alanin.out.energy
restartfile alanin.out



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
  }
}