1firststep 0 2numsteps 10 3 4seed 1234 5 6#usecharmm28parfile yes 7 8posfile UA_butane.pdb 9psffile UA_butane.psf 10parfile UA_butane.par 11temperature 300 12 13Screen false 14 15outputfreq 10 16 17dihedralsOutputFreq 1 18dihedralsFile UA_butane.out.dihedrals 19dihedralsIndex 0 20dihedralsSet false 21dihedralsSetfile none 22 23#finpdbposfile final.pdb 24#dofinpdbposfile false 25 26allenergiesfile UA_butane.out.energy 27 28dodcdfile false 29dcdoutputfreq 1 30dcdfile UA_butane.out.dcd 31 32boundaryConditions Normal 33 34cellManager Cubic 35cellsize 6.5 36 37 38Integrator { 39 level 0 Leapfrog { 40 timestep 1.0 41 force Improper 42 force Dihedral 43 force Bond 44 force Angle 45 force LennardJones 46 -algorithm NonbondedCutoff 47 -switchingFunction C2 48 -switchon 0.1 49 -cutoff 6.5 50 force Coulomb 51 -algorithm NonbondedCutoff 52 -switchingFunction C1 53 -cutoff 6.5 54 } 55} 56 57