firststep 0 numsteps 1000 exclude scaled1-4 seed 1234 posfile bpti.pdb psffile bpti.psf parfile bpti.par temperature 0 outputfreq 1 #allenergiesfile bpti.out.energy boundaryConditions periodic cellBasisVector1 63.0 0.0 0.0 cellBasisVector2 0.0 50.0 0.0 cellBasisVector3 0.0 0.0 50.0 cellOrigin 0.0 0.0 0.0 cellManager Cubic cellsize 5.0 Integrator { level 0 Leapfrog { timestep 1 force time Improper force time Dihedral force time Bond force time Angle force time LennardJones -switchingFunction C2 -algorithm NonbondedCutoff -switchon 1.0 -cutoff 10.0 force time Coulomb -switchingFunction Shift -algorithm NonbondedCutoff -switchon 1.0 -cutoff 10.0 } }