Not 100% clear what you mean, but my guess is that you want the result of what you are doing at command line to look like the "model output" plot in the GUI, and what you are getting is something different.
If that is the case, then most likely the issue is the initial conditions for the model. The GUI automatically estimates initial conditions from data and uses them in the plot.
When you use sim at the command line, the initial conditions are set to 0 by default.
So to get the same plot for sim as in the GUI, you need to estimate and use initial conditions.
here is an example of what you could do:
load dryer2 % example data file shipping with System Identification Toolbox
dry = iddata(y2,u2,0.08); % create iddata object
arxmodel=arx(dry,[4 4 1]); %estimate arx441 model - use your own order as needed
x0=findstates(arxmodel,dry); % find initial condition
OPT = simOptions('InitialCondition',x0); % specify simulation option to use init.cond.
ssmodel=idss(arxmodel); % convert the model to idss to be able to specify initial condition
sim(ssmodel,dry,OPT) % simulate with initial condition
