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 13 14#finpdbposfile final.pdb 15#dofinpdbposfile false 16 17#Screen false 18outputfreq 1 19 20dodihedralsfile true 21dihedralsOutputFreq 1 22dihedralsFile UA_butane.out.dihedrals 23dihedralsIndex 0 24dihedralsSet false 25dihedralsSetfile none 26 27allenergiesfile UA_butane.out.energy 28 29dodcdfile false 30dcdoutputfreq 1 31dcdfile butane.out.dcd 32 33boundaryConditions Normal 34 35cellManager Cubic 36cellsize 6.5 37 38 39Integrator { 40 level 0 Leapfrog { 41 timestep 1.0 42 force Improper 43 force Dihedral 44 force Bond 45 force Angle 46 force LennardJones 47 -algorithm NonbondedCutoff 48 -switchingFunction C2 49 -switchon 0.1 50 -cutoff 6.5 51 force Coulomb 52 -algorithm NonbondedCutoff 53 -switchingFunction C1 54 -cutoff 6.5 55 } 56} 57 58