Duke 3D had no frame limiter, most DOS games didn't because they didn't think of computers as fast as modern ones I guess.
To solve your problem in DOSBox you could experiment around with the cycles variable in the dosboxDuke3D.conf file in the install folder of the GOG version. Standard is cycles=max, I'd start trying around with cycles=2000 or 3000.
When you have DOSBox running in windowed mode (switch with Alt+Return) the window title displays the current cycle count. To experiment around you can decrease that with Strg+F11 and increase it with Strg+F12 (Some slightly weird thing with DOSBox is that in the stanard config cyclesup and down have different values). Fiddle around with that till you find a cycles count that works for you and write that into the config. Perhaps write it also in the other dosbox.conf files in the folder.
Or you could simply use eduke32.