You could use a loop:
"make a macro file e.g kapis.mac and add the following
/gun/energy {eKin} MeV
/run/beamOn 100000
/control/shell youroutput.dat output_{eKin}.dat
then in geant4 command line paste this:
/control/loop kapis.mac eKin 10 100 20
assuming the initial energy denoted by variable ekin is 10kev and final is 100kev in steps of 20kev or so as you wish."