You can run simulation models programatically using the sim command. You can get the documentation for that by typing doc sim on your MATLAB command line. This allows you to specify name, value pairs. so for example
tStop = 30; % you could have additional code to determine stop time
simout = sim('myModel','StopTime',num2str(tStop)) % even numerical parameters must be sent as strings
It is a little more complicated using parsim. You have to first create simulink simulation object and then set its parameters. Something like this. I show it just for one model but you could do it in a loop for multiple model runs.
% make a simulink simulation input object
in = Simulink.SimulationInput('myModel')
% set the stop time parameter
tStop = 45; % you could have more code to determine stop time
in = in.setModelParameter('StopTime',num2str(45))
% run the simulation
simout = parsim(in)
